Receptor
PDB id Resolution Class Description Source Keywords
1BL5 2.5 Å EC: 1.1.1.42 ISOCITRATE DEHYDROGENASE FROM E. COLI SINGLE TURNOVER LAUE S OF RATE-LIMITED PRODUCT COMPLEX, 10 MSEC TIME RESOLUTION ESCHERICHIA COLI OXIDOREDUCTASE NAD(A)-CHOH(D) PHOSPHORYLATION
Ref.: MILLISECOND LAUE STRUCTURES OF AN ENZYME-PRODUCT CO USING PHOTOCAGED SUBSTRATE ANALOGS. NAT.STRUCT.BIOL. V. 5 891 1998
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AKG A:1;
Valid;
none;
submit data
146.098 C5 H6 O5 C(CC(...
MG A:418;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
NAP A:2;
Valid;
Atoms found LESS than expected: % Diff = 0;
submit data
743.405 C21 H28 N7 O17 P3 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1GRO 2.5 Å EC: 1.1.1.42 REGULATORY AND CATALYTIC MECHANISMS IN ESCHERICHIA COLI ISOC DEHYDROGENASE: MULTIPLE ROLES FOR N115 ESCHERICHIA COLI OXIDOREDUCTASE NADP PHOSPHORYLATION GLYOXYLATE BYPASS OXIDOREDUCTASE (NAD(A)-CHOH(D))
Ref.: SECOND-SITE SUPPRESSION OF REGULATORY PHOSPHORYLATI ESCHERICHIA COLI ISOCITRATE DEHYDROGENASE. PROTEIN SCI. V. 5 287 1996
Members (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 9ICD Kd = 125 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
2 4AJ3 - ICT C6 H8 O7 C(C(C(C(=O....
3 1PB1 - ICT C6 H8 O7 C(C(C(C(=O....
4 5ICD - ICT C6 H8 O7 C(C(C(C(=O....
5 4AJA - ICT C6 H8 O7 C(C(C(C(=O....
6 1AI3 Ki = 403 uM NDO C21 H27 N6 O18 P3 c1cc(c[n+]....
7 1ISO - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
8 1P8F - ICT C6 H8 O7 C(C(C(C(=O....
9 4AJB - TAP C21 H28 N7 O16 P3 S c1cc(c[n+]....
10 1CW4 - AKG C5 H6 O5 C(CC(=O)O)....
11 4BNP Ki = 96 uM ICT C6 H8 O7 C(C(C(C(=O....
12 1CW1 - ICT C6 H8 O7 C(C(C(C(=O....
13 1GRO Ki = 0.033 uM ICT C6 H8 O7 C(C(C(C(=O....
14 1IDE - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
15 4AJC - AKG C5 H6 O5 C(CC(=O)O)....
16 4AJS - ICT C6 H8 O7 C(C(C(C(=O....
17 1HJ6 - IPM C7 H12 O5 CC(C)C(C(C....
18 1BL5 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
19 1AI2 Ki = 2.7 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
20 1GRP Ki = 0.189 mM ICT C6 H8 O7 C(C(C(C(=O....
21 8ICD - ICT C6 H8 O7 C(C(C(C(=O....
70% Homology Family (23)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 9ICD Kd = 125 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
2 4AJ3 - ICT C6 H8 O7 C(C(C(C(=O....
3 1PB1 - ICT C6 H8 O7 C(C(C(C(=O....
4 5ICD - ICT C6 H8 O7 C(C(C(C(=O....
5 4AJA - ICT C6 H8 O7 C(C(C(C(=O....
6 1AI3 Ki = 403 uM NDO C21 H27 N6 O18 P3 c1cc(c[n+]....
7 1ISO - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
8 1P8F - ICT C6 H8 O7 C(C(C(C(=O....
9 4AJB - TAP C21 H28 N7 O16 P3 S c1cc(c[n+]....
10 1CW4 - AKG C5 H6 O5 C(CC(=O)O)....
11 4BNP Ki = 96 uM ICT C6 H8 O7 C(C(C(C(=O....
12 1CW1 - ICT C6 H8 O7 C(C(C(C(=O....
13 1GRO Ki = 0.033 uM ICT C6 H8 O7 C(C(C(C(=O....
14 1IDE - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
15 4AJC - AKG C5 H6 O5 C(CC(=O)O)....
16 4AJS - ICT C6 H8 O7 C(C(C(C(=O....
17 1HJ6 - IPM C7 H12 O5 CC(C)C(C(C....
18 1BL5 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
19 1AI2 Ki = 2.7 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
20 1GRP Ki = 0.189 mM ICT C6 H8 O7 C(C(C(C(=O....
21 8ICD - ICT C6 H8 O7 C(C(C(C(=O....
22 1HQS - CIT C6 H8 O7 C(C(=O)O)C....
23 2D4V - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
50% Homology Family (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 9ICD Kd = 125 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
2 4AJ3 - ICT C6 H8 O7 C(C(C(C(=O....
3 1PB1 - ICT C6 H8 O7 C(C(C(C(=O....
4 5ICD - ICT C6 H8 O7 C(C(C(C(=O....
5 4AJA - ICT C6 H8 O7 C(C(C(C(=O....
6 1AI3 Ki = 403 uM NDO C21 H27 N6 O18 P3 c1cc(c[n+]....
7 1ISO - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
8 1P8F - ICT C6 H8 O7 C(C(C(C(=O....
9 4AJB - TAP C21 H28 N7 O16 P3 S c1cc(c[n+]....
10 1CW4 - AKG C5 H6 O5 C(CC(=O)O)....
11 4BNP Ki = 96 uM ICT C6 H8 O7 C(C(C(C(=O....
12 1CW1 - ICT C6 H8 O7 C(C(C(C(=O....
13 1GRO Ki = 0.033 uM ICT C6 H8 O7 C(C(C(C(=O....
14 1IDE - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
15 4AJC - AKG C5 H6 O5 C(CC(=O)O)....
16 4AJS - ICT C6 H8 O7 C(C(C(C(=O....
17 1HJ6 - IPM C7 H12 O5 CC(C)C(C(C....
18 1BL5 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
19 1AI2 Ki = 2.7 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
20 1GRP Ki = 0.189 mM ICT C6 H8 O7 C(C(C(C(=O....
21 8ICD - ICT C6 H8 O7 C(C(C(C(=O....
22 1HQS - CIT C6 H8 O7 C(C(=O)O)C....
23 2D4V - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
24 1XKD - ICT C6 H8 O7 C(C(C(C(=O....
25 1TYO - ENP C17 H24 N5 O17 P3 c1cn2cnc3c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: AKG; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 AKG 1 1
2 SIN 0.526316 0.833333
3 SHF 0.416667 0.666667
4 3PY 0.409091 0.652174
Ligand no: 2; Ligand: NAP; Similar ligands found: 114
No: Ligand ECFP6 Tc MDL keys Tc
1 NAP 1 1
2 NA0 0.881356 0.986301
3 TAP 0.872881 0.934211
4 NDO 0.840336 0.972603
5 NAD 0.811966 0.986111
6 N01 0.733871 0.958904
7 A3D 0.712 0.972603
8 NBP 0.707692 0.935065
9 NAD IBO 0.688 0.921053
10 NHD 0.68254 0.958904
11 NJP 0.661417 0.972973
12 NAJ PYZ 0.659091 0.898734
13 NFD 0.658915 0.934211
14 DND 0.619048 0.959459
15 NXX 0.619048 0.959459
16 ZID 0.605839 0.972603
17 NAQ 0.59854 0.922078
18 ATR 0.59292 0.917808
19 NAE 0.591241 0.946667
20 NDE 0.58042 0.986301
21 A22 0.571429 0.958904
22 AMP NAD 0.571429 0.933333
23 NAJ 0.567164 0.986111
24 A2R 0.563025 0.932432
25 NDC 0.561644 0.922078
26 NA7 0.552846 0.907895
27 ODP 0.551471 0.935065
28 A2P 0.539823 0.930556
29 8ID 0.537313 0.910256
30 NPW 0.525547 0.8875
31 NZQ 0.521739 0.910256
32 CNA 0.521739 0.959459
33 NDP 0.514493 0.922078
34 PO4 PO4 A A A A PO4 0.503937 0.930556
35 1DG 0.503401 0.922078
36 DG1 0.503401 0.922078
37 NAD TDB 0.5 0.696078
38 TXP 0.5 0.922078
39 NMN AMP PO4 0.492958 0.921053
40 25L 0.492308 0.958904
41 25A 0.492063 0.972222
42 NAD NDT 0.490909 0.747368
43 NMN 0.486726 0.888889
44 NGD 0.485714 0.935065
45 2AM 0.477876 0.891892
46 ADP 0.458333 0.945205
47 PAP 0.451613 0.931507
48 ADP MG 0.45082 0.906667
49 ADP BEF 0.447154 0.883117
50 BEF ADP 0.447154 0.883117
51 A2D 0.445378 0.945205
52 SAP 0.44 0.896104
53 AGS 0.44 0.896104
54 ADP PO3 0.44 0.944444
55 M33 0.439024 0.906667
56 AR6 AR6 0.438849 0.945205
57 BA3 0.438017 0.945205
58 ATP MG 0.436508 0.906667
59 ADP BMA 0.43609 0.92
60 OAD 0.43609 0.92
61 ATP 0.435484 0.945205
62 B4P 0.434426 0.945205
63 AP5 0.434426 0.945205
64 GAP 0.433071 0.92
65 0WD 0.432432 0.922078
66 2A5 0.432 0.87013
67 5FA 0.432 0.945205
68 AQP 0.432 0.945205
69 00A 0.428571 0.909091
70 CA0 0.427419 0.92
71 ADP ALF 0.426357 0.871795
72 ALF ADP 0.426357 0.871795
73 ACP 0.424 0.92
74 NAJ PZO 0.423841 0.897436
75 ADP VO4 0.423077 0.932432
76 ANP MG 0.423077 0.896104
77 V3L 0.421875 0.945205
78 ACQ 0.421875 0.92
79 ADQ 0.421053 0.92
80 APR 0.420635 0.918919
81 AR6 0.420635 0.918919
82 ATP A A A 0.42029 0.958333
83 CO7 0.419753 0.786517
84 1ZZ 0.419118 0.841463
85 3OD 0.419118 0.92
86 DLL 0.41791 0.958904
87 AD9 0.417323 0.92
88 OVE 0.416667 0.857143
89 NAX 0.416667 0.875
90 MYR AMP 0.416058 0.841463
91 AV2 0.415385 0.868421
92 A3P 0.414634 0.944444
93 NNR 0.414414 0.72973
94 ALF ADP 3PG 0.413793 0.8625
95 LA8 ALF 3PG 0.413793 0.8625
96 ANP 0.410853 0.92
97 A1R 0.410448 0.860759
98 ABM 0.409836 0.893333
99 A 0.408333 0.944444
100 AMP 0.408333 0.944444
101 SON 0.408 0.933333
102 5AL 0.407692 0.932432
103 PPS 0.407692 0.829268
104 NAI 0.406897 0.909091
105 DAL AMP 0.406015 0.932432
106 ADX 0.404762 0.829268
107 ATF 0.40458 0.907895
108 AMP DBH 0.404255 0.894737
109 139 0.402685 0.875
110 AMP MG 0.401639 0.893333
111 50T 0.401575 0.906667
112 SRP 0.401515 0.907895
113 3AM 0.4 0.90411
114 FA5 0.4 0.933333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1GRO; Ligand: ICT; Similar sites found: 18
This union binding pocket(no: 1) in the query (biounit: 1gro.bio1) has 47 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc)
1 3TY3 GGG 0.00004539 0.58616
2 1A05 IPM 0.0001017 0.56737
3 1HEX NAD 0.0000001241 0.46869
4 2UXR ICT 0.005345 0.46761
5 4OWK NGA 0.0203 0.43905
6 3QDW NDG 0.03427 0.42784
7 3QDW NDG 0.03427 0.42784
8 3QDW NDG 0.03501 0.42718
9 2XG5 EC5 0.02678 0.42541
10 2XG5 EC2 0.02678 0.42541
11 2ZQO NGA 0.04147 0.42438
12 4OWK NGA 0.04307 0.42264
13 4OWK NGA 0.04307 0.42264
14 3QDU CBS CBS 0.04864 0.41786
15 4BHL ARG 0.02276 0.41768
16 4C2C ALA ALA ALA 0.04513 0.41139
17 2Z4T C5P 0.0448 0.40865
18 1GNW GTX 0.04121 0.40105
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