Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DED A:301;
B:302;
Valid;
Valid;
none;
none;
Kd < 0.12 nM
249.096 C4 H13 N O7 P2 CN(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: DED; Similar ligands found: 15
No: Ligand ECFP6 Tc MDL keys Tc
1 DED 1 1
2 P23 0.558824 0.688889
3 IPR 0.5 0.772727
4 IPE 0.487179 0.653061
5 P25 0.487179 0.666667
6 P22 0.470588 0.6
7 43W 0.461538 0.630435
8 0CH 0.461538 0.625
9 EIP 0.452381 0.717391
10 0CJ 0.452381 0.666667
11 0JX 0.45 0.644444
12 0K2 0.439024 0.630435
13 BHI 0.431818 0.66
14 MGM 0.431034 0.862745
15 0O3 0.428571 0.6
Similar Ligands (3D)
Ligand no: 1; Ligand: DED; Similar ligands found: 120
No: Ligand Similarity coefficient
1 DMA 0.9793
2 IS3 0.9531
3 0CN 0.9424
4 2JA 0.9321
5 0CG 0.9238
6 ISY 0.9214
7 PMV 0.9193
8 10G 0.9109
9 RGP 0.9107
10 DST 0.9079
11 10E 0.9073
12 STX 0.9070
13 43Q 0.9023
14 DG2 0.9011
15 H6P 0.9010
16 GAE 0.9007
17 AGP 0.8987
18 DXP 0.8958
19 DI9 0.8950
20 6FR 0.8932
21 ZZU 0.8920
22 58X 0.8918
23 4TP 0.8916
24 AZM 0.8903
25 ATX 0.8897
26 G88 0.8886
27 3CX 0.8885
28 DLT 0.8876
29 RES 0.8848
30 2OR 0.8848
31 0ON 0.8845
32 68B 0.8831
33 5SP 0.8820
34 5DL 0.8819
35 PAU 0.8811
36 3PO 0.8806
37 5LD 0.8803
38 ARG 0.8800
39 PA5 0.8796
40 2E4 0.8793
41 GHQ 0.8789
42 PRO GLY 0.8787
43 7O4 0.8786
44 HPO 0.8783
45 2E6 0.8780
46 MLY 0.8772
47 M5B 0.8771
48 2E5 0.8771
49 6C9 0.8768
50 NLQ 0.8765
51 HSA 0.8763
52 SSC 0.8758
53 DX5 0.8755
54 MZM 0.8752
55 EGV 0.8752
56 5RP 0.8743
57 G14 0.8742
58 0CM 0.8739
59 G6Q 0.8738
60 VFG 0.8736
61 A5P 0.8734
62 NFZ 0.8732
63 DER 0.8729
64 M3L 0.8725
65 XOG 0.8724
66 GGB 0.8715
67 6HN 0.8705
68 D1G 0.8703
69 M3C 0.8697
70 5TO 0.8690
71 HCA 0.8684
72 PTB 0.8684
73 GVA 0.8683
74 HJ7 0.8680
75 S0E 0.8671
76 I58 0.8670
77 GRQ 0.8669
78 PAN 0.8667
79 LVD 0.8664
80 PML 0.8661
81 EUE 0.8655
82 CUW 0.8653
83 BGT 0.8638
84 4NS 0.8635
85 BSA 0.8634
86 8SZ 0.8632
87 8V8 0.8631
88 F90 0.8630
89 SB7 0.8625
90 GNW 0.8624
91 14W 0.8623
92 HPP 0.8620
93 DI6 0.8618
94 ODK 0.8605
95 36M 0.8604
96 3YP 0.8604
97 9W5 0.8604
98 7UC 0.8599
99 PPK 0.8598
100 S6P 0.8598
101 1PS 0.8596
102 DAR 0.8596
103 NFA 0.8594
104 HS7 0.8589
105 Q06 0.8587
106 TX4 0.8581
107 ENO 0.8570
108 GLY GLY GLY 0.8570
109 4NP 0.8568
110 VGS 0.8566
111 G01 0.8564
112 OOG 0.8559
113 KAP 0.8558
114 R5P 0.8548
115 6C8 0.8540
116 5H6 0.8535
117 VFM 0.8532
118 ING 0.8531
119 HCT 0.8526
120 GG8 0.8504
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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