Receptor
PDB id Resolution Class Description Source Keywords
1Q54 1.93 Å EC: 5.3.3.2 STRUCTURE AND MECHANISM OF ACTION OF ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE I SOMERASE: COMPLEX WITH THE BROMOHYDRINE OF IPP ESCHERICHIA COLI COMPLEX ISOMERASE
Ref.: STRUCTURE AND MECHANISM OF ACTION OF ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE ISOMERASE. J.AM.CHEM.SOC. V. 125 3198 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BHI A:301;
B:302;
Valid;
Valid;
none;
none;
Ki = 1.4 uM
343.003 C5 H13 Br O8 P2 C[C@@...
MG A:401;
B:401;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
MN A:201;
B:201;
Part of Protein;
Part of Protein;
none;
none;
submit data
54.938 Mn [Mn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1NFS 1.96 Å EC: 5.3.3.2 STRUCTURE AND MECHANISM OF ACTION OF ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE I SOMERASE: COMPLEX WITH NIPP ESCHERICHIA COLI COMPLEX ISOMERASE
Ref.: CATALYTIC MECHANISM OF ESCHERICHIA COLI ISOPENTENYL DIPHOSPHATE ISOMERASE INVOLVES CYS-67, GLU-116, AND TYR-104 AS SUGGESTED BY CRYSTAL STRUCTURES OF COMPLEXES WITH TRANSITION STATE ANALOGUES AND IRREVERSIBLE INHIBITORS J.BIOL.CHEM.
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2VNP Ki = 0.12 nM DED C4 H13 N O7 P2 CN(C)CCO[P....
2 1NFS Kd < 0.12 nM DED C4 H13 N O7 P2 CN(C)CCO[P....
3 1Q54 Ki = 1.4 uM BHI C5 H13 Br O8 P2 C[C@@](CCO....
4 1PPW ic50 ~ 50 uM EIP C5 H14 O8 P2 C[C@@H](CC....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2VNP Ki = 0.12 nM DED C4 H13 N O7 P2 CN(C)CCO[P....
2 1NFS Kd < 0.12 nM DED C4 H13 N O7 P2 CN(C)CCO[P....
3 1Q54 Ki = 1.4 uM BHI C5 H13 Br O8 P2 C[C@@](CCO....
4 1PPW ic50 ~ 50 uM EIP C5 H14 O8 P2 C[C@@H](CC....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2VNP Ki = 0.12 nM DED C4 H13 N O7 P2 CN(C)CCO[P....
2 1NFS Kd < 0.12 nM DED C4 H13 N O7 P2 CN(C)CCO[P....
3 1Q54 Ki = 1.4 uM BHI C5 H13 Br O8 P2 C[C@@](CCO....
4 1PPW ic50 ~ 50 uM EIP C5 H14 O8 P2 C[C@@H](CC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: BHI; Similar ligands found: 10
No: Ligand ECFP6 Tc MDL keys Tc
1 BHI 1 1
2 DP6 0.644444 0.878049
3 FM0 0.470588 0.833333
4 P23 0.463415 0.775
5 IPR 0.454545 0.780488
6 DED 0.431818 0.66
7 PMV 0.425532 0.878049
8 0CH 0.422222 0.780488
9 P25 0.413043 0.785714
10 IPE 0.413043 0.767442
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1NFS; Ligand: DED; Similar sites found: 34
This union binding pocket(no: 1) in the query (biounit: 1nfs.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2O1C PPV 0.00006661 0.52367 None
2 4DSU BZI 0.006226 0.43285 None
3 5HZX 2GE 0.005288 0.42117 1.13636
4 5M6N 7H9 0.006011 0.43042 1.69492
5 4MTI 2DX 0.01915 0.40483 1.73913
6 3QPB URA 0.0147 0.40928 2.73224
7 4YJK URA 0.01676 0.40761 2.73224
8 1QVJ RP5 0.000843 0.47356 3.27869
9 5EXK MET 0.01045 0.41696 3.27869
10 2J5B TYE 0.01943 0.40502 3.27869
11 2I8T GDD 0.0006067 0.40018 3.59281
12 1RYA GDP 0.0004706 0.47165 3.75
13 3IHB GLU 0.008817 0.41658 3.82514
14 5T96 79J 0.01625 0.40655 3.82514
15 5LKC FUC GLA A2G 0.01296 0.40923 4.37158
16 5M6M 7H8 0.01183 0.40874 4.72441
17 5C83 4YN 0.01431 0.40466 5.45455
18 5ISY NAD 0.002611 0.43099 5.46448
19 2GPT TLA 0.006723 0.42796 5.46448
20 4RKX 3S9 0.008244 0.42121 5.46448
21 5EWK P34 0.02007 0.40192 5.46448
22 5LPG 71V 0.01081 0.41065 5.4878
23 3IWD M2T 0.01688 0.40549 5.88235
24 2VSL MAA LYS PRO PHE 0.00975 0.41285 6.25
25 5GG9 8GT 0.0008197 0.44451 6.55738
26 4YVN EBS 0.02087 0.40376 6.55738
27 3CM2 X23 0.01001 0.41696 7.69231
28 5KJW 53C 0.01177 0.41491 8.74317
29 1UGY GLA BGC 0.007833 0.41526 12.0301
30 5L2R MLA 0.007618 0.42478 12.5683
31 3O61 GDD 0.005163 0.41863 13.1148
32 5KOD IAC 0.02226 0.40839 15.3005
33 3GZ8 APR 0.0005656 0.46051 16.6667
34 3I7V ATP 0.004604 0.42927 17.1642
Pocket No.: 2; Query (leader) PDB : 1NFS; Ligand: DED; 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: 1nfs.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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