Glyco-Chemistry and the PDB
Glycoconjugates
( excluding Glycoproteins)
CELLULOSE Fragments in PDB
ABL 5-amino-5-deoxy-cellobiono-1,5-lactam di-saccharide
CBI CELLOBIOSE di-saccharide
CE5 CELLOPENTAOSE penta-saccharide
CE6 CELLOHEXAOSE hexa-saccharide
CE8 CELLOOCTAOSE octa-saccharide
CTR CELLOTRIOSE tri-saccharide
CTT CELLOTETRAOSE tetra-saccharide
DCB 2,4-DINITROPHENYL-2-DEOXY-2-FLUOROBETA-D-CELLOBIOSIDE di-saccharide
FCT DEOXY-2-FLUORO-B-D-CELLOTRIOSIDE tri-saccharide
FFC 2-DEOXY-2-FLUORO-B-D-CELLOBIOSIDE di-saccharide
RCB "p-nitrophenyl beta-D-cellotrioside" tri-saccharide
TCB THIOCELLOBIOSE di-saccharide
http://en.wikipedia.org/wiki/Cellobiose
http://en.wikipedia.org/wiki/Cellulose
Chitin
long-chain polymer of a N-acetylglucosamine, main
component of the cell walls of fungi, the exoskeletons
of arthropods and insects http://en.wikipedia.org/wiki/Chitin
CTO TRIACETYLCHITOTRIOSE tri-saccharide
GUM 4-METHYL-UMBELLIFERYL-N-ACETYL-CHITOBIOSE di-saccharide
CTO
Umbelliferone can be used as a
fluorescence dye
http://en.wikipedia.org/wiki/Umbelliferone
GUM
Glycoconjugates




Covalent bond between carbohydrate and biomolecule
Glycoproteins
Glycolipids
Function of oilgosaccharides:
 Structural
Hydrophilic (protein surface)
Limit conformations
 Reactivity
Shield surface and affect reactivity
 Surface Recognition
Label proteins
Intracellular communication
http://en.wikipedia.org/wiki/Glycoconjugate
Glycoproteins: 2 types(?)
Proteoglycans have not been considered as glycoproteins
because their carbohydrate seemed to differ so greatly
1. Proteoglycans are proteins that are heavily glycosylated. The
basic proteoglycan unit consists of a "core protein" with one or
more covalently attached glycosaminoglycan (GAG) chain(s). Serlinked and consist of long, unbranched chains of alternating
residues of hexosamine and uronic acid or galactose, often
sulfated found mainly in connective tissues
http://en.wikipedia.org/wiki/Proteoglycan
2. Glycoproteins are proteins that contain oligosaccharide chains
(glycans) covalently attached to polypeptide side-chains. Nglycosylation and O-glycosylation with comparatively small,
branched, usually unsulfated carbohydrate units, devoid of
repeating units.
http://en.wikipedia.org/wiki/Glycoprotein
Proteoglycans
Glycoproteins
Carbohydrate Composition =
up to 97%
Carbohydrate Composistion =
1- 60%
1-100’s of GAG chains
Short, branched, N and O-linked
carbohydrate chains < 20
residues
GAG chains of 80 sugars
Mixture of sugars
No sialic acid
Often terminal sialic acid
Up to 3 x 10 Kd
Up to 2 - 300 Kd
GAG Glycosaminoglycan
http://en.wikipedia.org/wiki/Glycosaminoglycan
Simple Glycoconjugates: Glycosides are
widely distributed in plants
http://en.wikipedia.org/wiki/Glycoside
The most important glycosides:
Non-toxic: Flavonoids
Anthocyans
Tannins
Toxic: Cyanogennic glycosides
Saponin that form soapy lathers when mixed and agitated
with water, used in detergents, foaming agents, and
emulsifiers. http://en.wikipedia.org/wiki/Saponin
Coumarins produced synthetically and widely used in
perfumes.
DGX DIGOXIN digitalis, is a purified cardiac glycoside
and extracted from the foxglove plant
http://en.wikipedia.org/wiki/Digoxin
PDB entry has only
mono-saccharide part
Related PDB OBN OUABAIN
poisonous cardiac glycoside
http://en.wikipedia.org/wiki/Cardiac_glycoside
http://en.wikipedia.org/wiki/Ouabain
RUT RUTIN di-saccharide citrus flavonoid
glycoside inhibits platelet aggregation
http://en.wikipedia.org/wiki/Rutin
FSC
Fusicoccin
Fungal Toxin
http://en.wikipedia.org/wiki/Fusicoccin
Glycosaminoglycans
Proteoglycans
Polysaccharides in PDB
Fibre Diffraction
3hya HYALURONIC ACID
GCU NAG BDP NAG BDP NAG BDP NAG
1kes KERATAN SULPHATE
G6S NGS G6S NGS
1aga AGAROSE
GAL AAL GAL AAL GAL AAL
1c4s CHONDROITIN-4-SULFATE
GC4 ASG GCU ASG GC4 ASG
1cap CAPSULAR POLYSACCHARIDE
MAN BGC BDP GAL MAN CEG MAN BGC BDP GAL MAN CEG
1car I-CARRAGEENAN
G4S DGS G4S DGS G4S DGS
2c4s CHONDROITIN 4-SULFATE
GCU ASG GCU ASG
2hya HYALURONIC ACID
GCU NAG GCU NAG GCU NAG GCU NAG
4hya HYALURONIC ACID
NAG GCU NAG GCU NAG GCU
Download expanded fibre diffraction
result from TVECT record
http://www.ebi.ac.uk/pdbe/pqs/macmol/1foo.mmol
rasmol 1foo.mmol
1c4s
sulfated
glycosaminoglycan
(GAG) found attached
to proteins as part of
a proteoglycan.
http://en.wikipedia.org/wiki/Chondroitin_sulfate
1kes
Keratan are
sulfated
glycosaminoglyc
ans found in the
cornea, cartilage,
and bone
http://en.wikipedia.org/wiki/Keratan_sulphate
Heparin
 Heparin activates antithrombin III (AT-III), a
serine protease inhibitor that blocks thrombin
and factor Xa in the coagulation cascade. It
binds to AT-III very specifically and with high
affinity.
 However, the composition of this drug,
consisting of a highly heterogeneous mixture
of polysaccharides, is ill defined.
 A synthetic heparin (pentasaccharide) named
Fondaparinux, was eventually developed.
http://en.wikipedia.org/wiki/Heparin
A portion of the structure of heparin
a glycosaminoglycan
most common disaccharide unit is composed of a
2-O-sulfated iduronic acid and
6-O-sulfated, N-sulfated glucosamine,
IdoA(2S)-GlcNS(6S)
IN PDB
H1S "HEPARIN DISACCHARIDE I-S" di-saccharide
H3S "HEPARIN DISACCHARIDE III-S" di-saccharide
NT1 "HEPARIN HEPTASACCHARIDE" hepta-saccharide
NTP "HEPARIN PENTASACCHARIDE" penta-saccharide
NTO TRISULFOAMINO HEPARIN PENTASACCHARIDE
HEPARIN SOLUTION SCATTERING
Alternating sulfated- glucosamine & sulfated iduronic acid
3iri (SGN IDS)9
3irj (SGN IDS)12
3irk (SGN IDS)15
3irl (SGN IDS)18
Oligosaccharides as drugs
Antibiotics
1.
2.
3.
4.
5.
6.
Polyketide – Antibiotics
Glycopeptide antibiotic
Aminoglycoside Anthracycline
Glycosidic antibiotics
Calichemicins and Esperamicins
Aminoglycoside antibiotics
Group 1
Sugar(s) attached
to ring system
(from 10 to 20
membered ring)
Macrolactone,
Polyketide Antibiotics
Polyketide antibiotics, antifungals,
cytostatics, anticholesteremic,
antiparasitics, coccidiostats, animal growth
promoters and natural insecticides are in
commercial use
http://en.wikipedia.org/wiki/Polyketide
NOTE in these slides reference is made to family files
e.g. FAM_000087. These are ‘super’ chem-comp CIF
files grouping sets of molecules into classes with
various properties listed.
Glycopeptide antibiotics
http://en.wikipedia.org/wiki/Glycopeptide_antibiotic
FAM_000087 & FAM_000407
Chloroorienticin A
VANCOMYCIN
Decaplanin
A40926
Teicoplanin
Balhimycin
Deglucobalhimycin
Not all ring
systems with
sugars attached
are Macrolydes
polyketide macrolactams
Immunosuppressant
FAM_000022
587 C32-O-(1-METHYL-INDOL-5-YL)18-HYDROXY-ASCOMYCIN
818 18-HYDROXYASCOMYCIN
858 C32-O-(1-ETHYL-INDOL-5-YL)ASCOMYCIN
FK5 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN
FKA BENZYL-CARBAMIC ACID[8-DEETHYL-ASCOMYCIN-8YL]ETHYL ESTER
Ketolide-Macrolide antibiotic
FAM_000042 ERY
FAM_000037 CAI
FAM_000047 NRB
FAM_000055 SPR
FAM_000067 XBK
FAM_000076 E7B
ERYTHROMYCIN A
CARBOMYCIN A
NARBOMYCIN
SPIRAMYCIN I
4,5-deepoxypimaricin antifungal
TAUTOMYCIN Polyketide
inhibitor of the protein phosphatases
PP1 and PP2A
SPR SPIRAMYCIN I 16-membered ring
macrolide aminoglycoside erythromycincarbomycin group
http://en.wikipedia.org/wiki/Spiramycin
Group 2
Glycosylated
relatives of
anthracycline
family that is
given as a
treatment for
some types of
cancer e.g.
Daunomycin
Aminoglycoside Anthracycline
Antineoplastic/Antibiotic
FAM_000019
BIS-DAUNORUBICIN
DAUNOMYCIN
2'-BROMO-4'-EPIDAUNORUBICIN
4-METHYLBENZYL-N-BIS[DAUNOMYCIN]
6-DEOXYDAUNOMYCIN
N-HYDROXYMETHYL-N-(2-METHOXYETHYL)-DAUNOMYCIN
4'-EPI-4'-(2-DEOXYFUCOSE)DAUNOMYCIN
http://en.wikipedia.org/wiki/Daunorubicin
http://en.wikipedia.org/wiki/Anthracycline
Aminoglycoside
Anthracycline
Daunomycin
intercalated in DNA
(PDB ID 1JO2)
FAM_000002 Aminoglycosides Anthracyclines Antibiotics Antineoplastic
DM2 DOXORUBICIN
DM6 4'-EPIDOXORUBICIN
DM7 4'-DEOXY-4'-IODODOXORUBICIN
NOD N-ETHYLHYDROXY-DOXORUBICIN
DMM 3'-DESAMINO-3'-(2-METHOXY-4-MORPHOLINYL)-DOXORUBICIN
DM4 1-O-DEMETHYL-6-DEOXYDOXORUBICIN
44D 7-[5-(4-AMINO-5-HYDROXY-6-METHYL-TETRAHYDRO-PYRAN-2YLOXY)-4-HYDROXY-6-METHYL-TETRAHYDRO-PYRAN-2-YLOXY]6,9,11-TRIHYDROXY-9-(2-HYDROXY-ACETYL)-7,8,9,10TETRAHYDRO-NAPHTHACENE-5,12-DIONE
CMD 3'-DESAMINO-3'-(3-CYANO-4-MORPHOLINYL)-DOXORUBICIN
FAM_000004 oligosaccharide anthracycline, chymotrypsin inhibitor
AKA 10-DECARBOXYMETHYLACLACINOMYCIN A
AKT 10-DECARBOXYMETHYLACLACINOMYCIN T
AKY ACLACINOMYCIN Y
FAM_000007 anthracycline Antitumor antibiotic
DRA 11-DEOXY-BETA-RHODOMYCIN
ERT METHYL (4R)-2-ETHYL-2,5,12-TRIHYDROXY-7-METHOXY-6,11-DIOXO-4{[2,3,6-TRIDEOXY-3-(DIMETHYLAMINO)-BETA-D-RIBOHEXOPYRANOSYL]OXY}-1H,2H,3H,4H,6H,11H-TETRACENE-1CARBOXYLATE
anthracycline Antitumor antibiotic
DRA
http://www.druglead.com/cds/Rhodomycins.html
Glycosidic antibiotics
e.g. Mithramycin and Chromycin in PDB entries
146d, 207d, 1bp8, 1d83, 1vaq, 1ekh
In FAM_000066.cif
DNA binding usually represented as LINKed
residues http://en.wikipedia.org/wiki/Plicamycin
http://en.wikipedia.org/wiki/Neomycin
Glycosidic antibiotics
Mithramycin 1
Mithramycin 2
Mg
Mithramycin 2
Mithramycin 1
Minor groove
Mithramycin
Two copies of the molecule binds in the minor groove of
the DNA and interacts with it via a Mg ion. (PDB ID 146d)
Calichemicins and Esperamicins
class of potent antitumor antibiotics
In PDB entries 2l65, 2pik, 1qms, 3oth, 3oti, 2gkc
In FAM_000068.cif & FAM_000070.cif (1pik)
http://en.wikipedia.org/wiki/Calicheamicin
Calichemicins
2pik
Enediyne antibiotic
DNA minor groove binder
Aminoglycoside antibiotics
Streptomycin in PDB entries 3hav, 1ntb,1nta, 1fjg
and in FAM_000056.cif
http://en.wikipedia.org/wiki/Streptomycin
Aminoglycoside antibiotics
http://en.wikipedia.org/wiki/Tobramycin
Tobramycin
In PDB entries 1tob,
2tob, 1lc4, 1m4d
In FAM_000072.cif
AO3 ALLOSAMIDIN di-saccharide
INSECTICIDE
Allosamidin is an
inhibitor of both insect
and bacterial chitinases.
Recently Allosamidin has
been reported to be an
inhibitor of acidic
mammalian chitinase an
observation which may
have implications in the
treatment of asthma.
type 2 diabetes mellitus
e.g. ACR in PDB 1agm, 1esw, 1gah,
1k1y, 1kxh, 1lf9, 1mxd,
1mxg, 1ulv, 2ecp, 2f6d,
2owc, 2oww, 2qmj,
2zq0, 3aic, 3bc9, 3jyr,
3jzj, 3k8m ,3pha, 3poc
Acarbose is an anti-diabetic drug
used to treat type 2 diabetes
mellitus
alpha-amylase inhibitor
3SA "ACARBOSE DERIVED TRISACCHARIDE" tri-saccharide
5SA "ACARBOSE DERIVED PENTASACCHARIDE" penta-saccharide
6SA "ACARBOSE DERIVED HEXASACCHARIDE" hexa-saccharide
AAO "ACARBOSE DERIVED HEXASACCHARIDE" hexa-saccharide
ABC "MODIFIED ACARBOSE HEXASACCHARIDE" hexa-saccharide
ABD "ACARBOSE DERIVED HEXASACCHARIDE" hexa-saccharide
ACR ALPHA-ACARBOSE tetra-saccharide
ARE "ACARBOSE DERIVED PENTASACCHARIDE" penta-saccharide
GAC DIHYDRO-ACARBOSE tetra-saccharide
IAB ISO-ACARBOSE tetra-saccharide
QPS BETA-ACARBOSE tetra-saccharide
ACG MODIFIED ACARBOSE PENTASACCHARIDE penta-saccharide
http://en.wikipedia.org/wiki/Acarbose
Glycolipids
 Cerebrosides
 Galactocerebroside – in neuronal membranes
 Glucocerebrosides – elsewhere in the body
 Sulfatides or sulfogalactocerebrosides
 A sulfuric acid ester of galactocerebroside
 Globosides: ceramide oligosaccharides
 Lactosylceramide
 Gangliosides
 Have a more complex oligosaccharide attached
 Biological functions: cell-cell recognition; receptors for
hormones
Group 3
Clue look at pdb 1qff
Any thing that looks
vaguely like a
Lipopolysaccharide
 Membrane lipids
 Hydrophilic heads are
oligosaccharides
 Recognition sites
Bacterial
Lipopolysaccharides
LINK
LINK
LINK
LINK
LINK
LINK
LINK
LINK
LINK
LINK
LINK
LINK
LINK
LINK
LINK
LINK
LINK
LINK
N2
C3
O1
N2
C3
O4
O3
O3
O4
O4
O6
C1
C2
C1
C1
C1
O5
C1
PA1
PA1
PA1
GCN
GCN
GCN
FTT
FTT
GMH
GMH
GCN
GCN
KDO
GLC
GLA
GLC
KDO
GMH
X1000
X1000
X1000
X1001
X1001
X1001
X1011
X1013
X1004
X1005
X1001
X1001
X1003
X1006
X1008
X1007
X1002
X1005
C1
O1
P1
C1
O1
P
C1
C1
P
P
C2
O6
O4
O3
O6
O3
C1
O3
FTT
FTT
DPO
FTT
FTT
PO4
DAO
MYR
EAP
PO4
KDO
PA1
KDO
GMH
GLC
GLC
GMH
GMH
PDB entry 1qff
X1009
X1010
X2000
X1011
X1013
X2001
X1012
X1014
X2004
X2005
X1002
X1000
X1002
X1005
X1006
X1006
X1004
X1004
E55 ERITORAN di-saccharide drug for the
treatment of severe sepsis
http://en.wikipedia.org/wiki/Eritoran
Lipopolysaccharides
 Occurs on the outer membrane of
gram-negative bacteria (e.g.: E. coli,
Salmonella typhimurium)
 Prime targets of antibodies
 Some bacterial polysaccharides are
toxic to humans
Bacterial Cell Walls
The NAM-NAG polysaccharide is in turn crosslinked by small peptides
 in Staphylococcus aureus, the cross link is a
tetrapeptide
 this tetrapeptide is unusual in that it contains
two amino acids of the D-series, namely D-Ala
and D-Gln
 each tetrapeptide is cross linked to an
adjacent tetrapeptide by a pentapeptide of five
glycine units
http://en.wikipedia.org/wiki/Peptidoglycan
Large polymers composed of alternating beta(1-4)linked N-acetylglucosamine (GlcNAc) and Nacetylmuramic acid (MurNAc) residues, which are
cross-linked by short peptide bridges. Lysine is
commonly the third amino acid of the peptide
moieties of PGN of Gram-positive bacteria while
Gram-negative bacteria have a diaminopimelic acid
(DAP) residue at this position.
N-Acetylglucosamine (NAG)
N-Acetylmuramic acid (NAM)
D-Isoglutamate
L-Ala
L-Lys
D-Ala
Bacterial Cell Walls
Lysozyme
The peptidoglycan of a
bacterial cell wall
Penicillin
Gram-positive Cells
In Gram-positive cells, peptidoglycan makes up as
much as 90% of the thick, compact cell wall, which is
the outermost structure.
Gram-negative Cells
The cell walls of Gram - bacteria are more chemically
complex, thinner and less compact. Peptidoglycan
makes up only 5-20% of the cell wall, and is not the
outermost layer, but lies between the plasma membrane
and an outer membrane.
Sepsis is a severe illness in which the
bloodstream is overwhelmed by
bacteria.
The primary difference between the
immunopathogenesis of Gram-positive and negative
sepsis lies in their causative agents. In the case of
Gram-negative bacteria, endotoxin (a lipopolysaccaride)
has been identified as the causative agent.
Endotoxin is absent in Gram-positive bacteria, instead
the cell wall contains a thick layer of peptidoglycan.
Lipoteichoic acids are embedded in the PGN layer and
these bacterial cell wall components are capable of
inducing the production of pro-inflammatory cytokines
to induce various pathways causing sepsis.
http://en.wikipedia.org/wiki/Sepsis
AMU BETA-N-ACETYLMURAMIC ACID
NAG N-ACETYL-D-GLUCOSAMINE
9lyz BACTERIAL CELL WALL TRISACCHARIDE
AMU NAG AMU
Weird PDB Protein not deposited
AMU BETA-N-ACETYLMURAMIC ACID
GMA 4-AMIDO-4-CARBAMOYL-BUTYRIC ACID
DAL D-ALANINE
NH2 AMINO GROUP
2aph MURAMYL PENTAPEPTIDE
AMU ALA GMA LYS DAL DAL NH2
Recommended Reading
Nature Reviews Drug Discovery,
9 308-324 (April 2010)
Definitions
http://www.chem.qmul.ac.uk/iupac/misc/glycp.html
TASKS
Look up the classes of glyco-chemistry listed here
and report on their occurrance in the PDB and their
binding, their natural source and uses
1. Simple Glycosides
(e.g. 7CA ICARISID II is another flavonoid glycoside)
2. The antibiotic classes and any more members
(e.g. IVM IVERMECTIN is an antiparasitic)
3. Lipopolysaccharides as drugs/metabolites
4. Other Carbohydrates as drugs and toxins
(e.g. PXT PECTENOTOXIN-2)