Receptor
PDB id Resolution Class Description Source Keywords
1OJM 1.78 Å EC: 4.2.2.1 SPECIFICITY AND MECHANISM OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE: COMPLEX WITH UNSULPHATED CHONDROITIN D ISACCHARIDE STREPTOCOCCUS PNEUMONIAE LYASE PROTEIN-CARBOHYDRATE COMPLEX
Ref.: STRUCTURES OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE IN COMPLEX WITH CHONDROITIN AND CHONDROITIN SULFATE DISACCHARIDES: INSIGHTS INTO SPECIFICITY AND MECHANISM OF ACTION J.BIOL.CHEM. V. 278 50596 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GCD NGA A:900;
Valid;
none;
submit data
378.31 n/a O=C([...
SO4 A:1200;
A:1201;
A:1202;
A:1203;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1W3Y 1.65 Å EC: 4.2.2.1 CRYSTAL STRUCTURE OF S. PNEUMONIAE HYALURONATE LYASE IN COMPLEX WITH PALMITOYL-VITAMIN C STREPTOCOCCUS PNEUMONIAE (ALFA5/ALFA5) BARREL LYASE PEPTIDOGLYCAN-ANCHOR
Ref.: L-ASCORBIC ACID 6-HEXADECANOATE, A POTENT HYALURONIDASE INHIBITOR: X-RAY STRUCTURE AND MOLECULAR MODELING OF ENZYME-INHIBITOR COMPLEXES J.BIOL.CHEM. V. 279 45990 2004
Members (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1LXK - NAG BDP NAG BDP n/a n/a
2 1OJM - GCD NGA n/a n/a
3 1W3Y ic50 = 100 uM PVC C22 H40 O8 CCCCCCCCCC....
4 1C82 - DGC NAG n/a n/a
5 2BRP ic50 > 100 uM SIE C24 H33 N3 O6 S2 CCCCCCCCCC....
6 1LOH - NAG BDP NAG BDP NAG BDP n/a n/a
7 1F9G Ki = 53 mM ASC C6 H8 O6 C([C@@H]([....
8 1OJN - GCD NG6 n/a n/a
9 1OJO - GCD ASG n/a n/a
10 1OJP - GCD NG6 n/a n/a
70% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1LXK - NAG BDP NAG BDP n/a n/a
2 1OJM - GCD NGA n/a n/a
3 1W3Y ic50 = 100 uM PVC C22 H40 O8 CCCCCCCCCC....
4 1C82 - DGC NAG n/a n/a
5 2BRP ic50 > 100 uM SIE C24 H33 N3 O6 S2 CCCCCCCCCC....
6 1LOH - NAG BDP NAG BDP NAG BDP n/a n/a
7 1F9G Ki = 53 mM ASC C6 H8 O6 C([C@@H]([....
8 1OJN - GCD NG6 n/a n/a
9 1OJO - GCD ASG n/a n/a
10 1OJP - GCD NG6 n/a n/a
50% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1LXM - NAG BDP NAG BDP NAG BDP n/a n/a
2 1I8Q - GC4 NAG n/a n/a
3 1LXK - NAG BDP NAG BDP n/a n/a
4 1OJM - GCD NGA n/a n/a
5 1W3Y ic50 = 100 uM PVC C22 H40 O8 CCCCCCCCCC....
6 1C82 - DGC NAG n/a n/a
7 2BRP ic50 > 100 uM SIE C24 H33 N3 O6 S2 CCCCCCCCCC....
8 1LOH - NAG BDP NAG BDP NAG BDP n/a n/a
9 1F9G Ki = 53 mM ASC C6 H8 O6 C([C@@H]([....
10 1OJN - GCD NG6 n/a n/a
11 1OJO - GCD ASG n/a n/a
12 1OJP - GCD NG6 n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GCD NGA; Similar ligands found: 38
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG GAD 1 1
2 NGA GCD 1 1
3 GCD NGA 1 1
4 GAD NDG 1 1
5 UCD 0.782609 0.979592
6 NG6 GCD 0.746667 0.761905
7 GCD NG6 0.746667 0.761905
8 NGK GCD 0.692308 0.746032
9 GCD ASG 0.692308 0.746032
10 GAL A2G 0.577465 0.88
11 A2G GAL 0.577465 0.88
12 GAL NGA 0.577465 0.88
13 NAG BDP 0.552632 0.959184
14 L42 0.547619 0.707692
15 FUC NAG 0.540541 0.88
16 HS2 0.5375 0.959184
17 NAG NGA 0.533333 0.865385
18 NAG A2G 0.533333 0.865385
19 ASG BDP ASG GCD 0.529412 0.723077
20 GAL NGA A2G 0.525641 0.849057
21 GC4 NAG 0.525 0.92
22 BGC RAM BGC GAD 0.494624 0.76
23 RAM GAD 0.486842 0.632653
24 DR3 0.470588 0.862745
25 NAG GAL FUC 0.470588 0.862745
26 NAG BDP NAG BDP 0.464646 0.924528
27 BEM MAV 0.461538 0.632653
28 NAG BDP NAG BDP NAG BDP 0.460784 0.942308
29 NAG GCU NAG GCU NAG GCU 5AX 0.442105 0.903846
30 NAG BDP NAG BDP NAG BDP NAG 0.442105 0.903846
31 AMU 0.434211 0.84
32 1GN ACY GAL ACY 1GN BGC GAL BGC 0.43299 0.865385
33 ACY 1GN GAL 1GN BGC ACY GAL BGC 0.43299 0.865385
34 MAW BEM BEM BEM 0.413793 0.62
35 MAW MAV GCU 0.413793 0.62
36 BEM MAV LGU MAV 0.413793 0.62
37 MAW LGU BEM BEM 0.413793 0.62
38 H3S 0.402174 0.661765
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1W3Y; Ligand: PVC; Similar sites found: 4
This union binding pocket(no: 1) in the query (biounit: 1w3y.bio1) has 37 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3DM0 GLC GLC 0.02833 0.4144 1.8732
2 4IFP MAL 0.0254 0.41693 2.7897
3 1HMU ASG GCD 0.00000001087 0.45993 32.8571
4 2E22 MAN 0.0000004297 0.41127 42.6813
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