Receptor
PDB id Resolution Class Description Source Keywords
1PPW 2.21 Å EC: 5.3.3.2 ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE ISOMERAS COMPLEX WITH THE BROMOHYDRINE OF IPP ESCHERICHIA COLI COMPLEX ISOMERASE
Ref.: A CRYSTALLOGRAPHIC INVESTIGATION OF PHOSPHOANTIGEN TO ISOPENTENYL PYROPHOSPHATE/DIMETHYLALLYL PYROPHOS ISOMERASE J.AM.CHEM.SOC. V. 127 536 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EIP A:301;
B:301;
 Valid;
Valid;
 none;
none;
 ic50 ~ 50 uM
264.107 C5 H14 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 ISOPENTENYLPYROPHOSPHAT DIMETHYLALLYLPYROPHOSPHATE ISOMERASE: COMPLEX WITH NIPP ESCHERICHIA COLI COMPLEX ISOMERASE
Ref.: CATALYTIC MECHANISM OF ESCHERICHIA COLI ISOPENTENYL DIPHOSPHATE ISOMERASE INVOLVES CYS-67, GLU-116, AND AS SUGGESTED BY CRYSTAL STRUCTURES OF COMPLEXES WIT TRANSITION STATE ANALOGUES AND IRREVERSIBLE INHIBIT J.BIOL.CHEM. V. 278 11903
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 (2D)
Ligand no: 1; Ligand: EIP; Similar ligands found: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 EIP 1 1
2 IPR 0.631579 0.864865
3 P23 0.487179 0.861111
4 3E9 0.457627 0.767442
5 IS3 0.454545 0.8
6 DED 0.452381 0.717391
7 ELU 0.45 0.767442
8 ELR 0.45 0.767442
9 0CH 0.44186 0.864865
10 IPE 0.431818 0.846154
11 P25 0.431818 0.868421
12 0O3 0.413043 0.820513
13 P22 0.410256 0.75
14 43W 0.409091 0.783784
15 0CJ 0.404255 0.820513
16 0JX 0.4 0.805556
Similar Ligands (3D)
Ligand no: 1; Ligand: EIP; Similar ligands found: 47
No: Ligand Similarity coefficient
1 BHI 0.9490
2 DMA 0.9251
3 H6P 0.9229
4 PMV 0.9167
5 2JA 0.9156
6 43Q 0.9128
7 STX 0.9093
8 ISY 0.9073
9 DST 0.9020
10 DX5 0.9000
11 0K2 0.8984
12 3CX 0.8961
13 PTB 0.8947
14 DLT 0.8931
15 6FR 0.8917
16 58X 0.8914
17 M3L 0.8836
18 API 0.8803
19 NFZ 0.8802
20 PUW 0.8785
21 XOG 0.8765
22 VFJ 0.8753
23 PAU 0.8752
24 0CG 0.8751
25 5TO 0.8742
26 VFG 0.8742
27 JF5 0.8717
28 AZM 0.8711
29 ZZU 0.8702
30 HPO 0.8685
31 HSA 0.8684
32 S7V 0.8674
33 6C9 0.8659
34 5H6 0.8644
35 DAR 0.8643
36 ARG 0.8641
37 2J3 0.8640
38 VGS 0.8622
39 FHV 0.8622
40 I58 0.8612
41 0ON 0.8612
42 68B 0.8598
43 PZX 0.8586
44 GLY GLY GLY 0.8566
45 0F3 0.8544
46 M6R 0.8536
47 M28 0.8532
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1NFS; Ligand: DED; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 1nfs.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1NFS; Ligand: DED; Similar sites found with APoc: 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 Sequence Similarity
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