Receptor
PDB id Resolution Class Description Source Keywords
4B5W 1.79 Å EC: 4.1.2.20 CRYSTAL STRUCTURES OF DIVALENT METAL DEPENDENT PYRUVATE ALDO MUTANT, HPAI, IN COMPLEX WITH PYRUVATE ESCHERICHIA COLI ATCC 8739 LYASE
Ref.: CRYSTAL STRUCTURE OF REACTION INTERMEDIATES IN PYRU CLASS II ALDOLASE: SUBSTRATE CLEAVAGE, ENOLATE STAB AND SUBSTRATE SPECIFICITY J.BIOL.CHEM. V. 287 36208 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:1258;
C:1254;
D:1255;
E:1257;
F:1256;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
CO A:1257;
B:1254;
C:1253;
D:1254;
E:1256;
F:1255;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
submit data
58.933 Co [Co+2...
PYR A:1259;
B:1255;
C:1255;
D:1256;
E:1258;
F:1257;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
Kd = 26.9 mM
88.062 C3 H4 O3 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4B5W 1.79 Å EC: 4.1.2.20 CRYSTAL STRUCTURES OF DIVALENT METAL DEPENDENT PYRUVATE ALDO MUTANT, HPAI, IN COMPLEX WITH PYRUVATE ESCHERICHIA COLI ATCC 8739 LYASE
Ref.: CRYSTAL STRUCTURE OF REACTION INTERMEDIATES IN PYRU CLASS II ALDOLASE: SUBSTRATE CLEAVAGE, ENOLATE STAB AND SUBSTRATE SPECIFICITY J.BIOL.CHEM. V. 287 36208 2012
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4B5V - PYR C3 H4 O3 CC(=O)C(=O....
2 4B5T - 2KT C4 H6 O3 CCC(=O)C(=....
3 4B5W Kd = 26.9 mM PYR C3 H4 O3 CC(=O)C(=O....
4 4B5S - PYR C3 H4 O3 CC(=O)C(=O....
5 4B5U - PYR C3 H4 O3 CC(=O)C(=O....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2V5K - OXM C2 H3 N O3 C(=O)(C(=O....
2 4B5V - PYR C3 H4 O3 CC(=O)C(=O....
3 4B5T - 2KT C4 H6 O3 CCC(=O)C(=....
4 4B5W Kd = 26.9 mM PYR C3 H4 O3 CC(=O)C(=O....
5 4B5S - PYR C3 H4 O3 CC(=O)C(=O....
6 4B5U - PYR C3 H4 O3 CC(=O)C(=O....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2V5K - OXM C2 H3 N O3 C(=O)(C(=O....
2 2VWT - PYR C3 H4 O3 CC(=O)C(=O....
3 4B5V - PYR C3 H4 O3 CC(=O)C(=O....
4 4B5T - 2KT C4 H6 O3 CCC(=O)C(=....
5 4B5W Kd = 26.9 mM PYR C3 H4 O3 CC(=O)C(=O....
6 4B5S - PYR C3 H4 O3 CC(=O)C(=O....
7 4B5U - PYR C3 H4 O3 CC(=O)C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PYR; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 PYR 1 1
2 ACY 0.636364 0.636364
3 OXD 0.545455 0.642857
4 KIV 0.411765 0.785714
5 AAE 0.411765 0.625
6 2KT 0.411765 0.733333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4B5W; Ligand: PYR; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4b5w.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4B5W; Ligand: PYR; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4b5w.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4B5W; Ligand: PYR; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4b5w.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4B5W; Ligand: PYR; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4b5w.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 4B5W; Ligand: PYR; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 4b5w.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 4B5W; Ligand: PYR; Similar sites found: 33
This union binding pocket(no: 6) in the query (biounit: 4b5w.bio1) has 35 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2BCG GER 0.03884 0.40507 1.5625
2 1C9K 5GP 0.03897 0.40137 1.66667
3 3NOJ PYR 0.009774 0.4303 1.68067
4 3CV2 OXL 0.0001292 0.54913 1.95312
5 3TUR DGL 0.02619 0.42104 1.95312
6 3TUR 6CL 0.04707 0.40633 1.95312
7 3MA0 XYP 0.0348 0.41319 2.34375
8 1Z6K OAA 0.0002311 0.52993 2.73438
9 1OFZ FUC 0.04163 0.40818 2.73438
10 2Q1A 2KT 0.04452 0.40744 2.73438
11 3W9F I3P 0.03531 0.40598 2.73438
12 3W6G FLC 0.02315 0.42322 2.77778
13 1D8C GLV 0.0006074 0.50387 3.125
14 1VBH PEP 0.0002225 0.53313 3.90625
15 2V2G BEZ 0.03641 0.40982 4.72103
16 1P7T PYR 0.0001286 0.53317 5.47196
17 3UNG ADP 0.03321 0.41042 6.25
18 2VOH CIT 0.02917 0.42273 7.00637
19 4L80 OXL 0.000006499 0.63438 7.8125
20 5J32 IPM 0.03921 0.40941 7.8125
21 1JQN DCO 0.001758 0.46559 8.20312
22 1GXU 2HP 0.02849 0.40201 8.79121
23 4IP7 FLC 0.0001116 0.54588 9.375
24 4KCT PYR 0.0001975 0.52562 9.76562
25 5E5U MLI 0.01648 0.45232 10.1562
26 2XZ9 PYR 0.00027 0.52833 10.5469
27 1SJN DUP 0.02194 0.40071 11.1765
28 2OG2 MLI 0.02578 0.4088 11.3281
29 3B9Q MLI 0.0454 0.40256 11.3281
30 2PL3 ADP 0.03092 0.41035 11.4407
31 2G50 PYR 0.0002821 0.53206 12.8906
32 1SGJ OAA 0.01559 0.41455 14.4531
33 1KC7 PPR 0.00002465 0.59001 17.1875
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