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Receptor
PDB id Resolution Class Description Source Keywords
4UMX 1.88 Å EC: 1.1.1.42 IDH1 R132H IN COMPLEX WITH CPD 1 HOMO SAPIENS OXIDOREDUCTASE ISOCITRATE DEHYDROGENASE INHIBITOR
Ref.: SELECTIVE INHIBITION OF MUTANT ISOCITRATE DEHYDROGE (IDH1) VIA DISRUPTION OF A METAL BINDING NETWORK BY ALLOSTERIC SMALL MOLECULE. J.BIOL.CHEM. V. 290 762 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL B:1416;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NAP B:1415;
A:1416;
Valid;
Valid;
none;
none;
submit data
743.405 C21 H28 N7 O17 P3 c1cc(...
VVS A:1415;
Valid;
none;
ic50 = 0.011 uM
366.5 C22 H30 N4 O CC(C)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4UMX 1.88 Å EC: 1.1.1.42 IDH1 R132H IN COMPLEX WITH CPD 1 HOMO SAPIENS OXIDOREDUCTASE ISOCITRATE DEHYDROGENASE INHIBITOR
Ref.: SELECTIVE INHIBITION OF MUTANT ISOCITRATE DEHYDROGE (IDH1) VIA DISRUPTION OF A METAL BINDING NETWORK BY ALLOSTERIC SMALL MOLECULE. J.BIOL.CHEM. V. 290 762 2015
Members (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 3INM - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 5SUN ic50 = 0.59 uM 70Q C24 H22 N4 O4 S CN(C)S(=O)....
3 6BKX - ICT C6 H8 O7 C([C@@H]([....
4 5YZH - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
5 4L06 Kd = 0.12 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
6 4UMY - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
7 6BL0 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
8 5DE1 ic50 = 46 nM 59D C28 H28 F N5 O3 C[C@@H]1CN....
9 6BL1 ic50 = 110 nM DWG C26 H24 N4 O C[C@H]1[C@....
10 5TQH ic50 = 0.02 uM 7J2 C23 H25 F N6 O2 Cc1cc(ccc1....
11 4UMX ic50 = 0.011 uM VVS C22 H30 N4 O CC(C)(C)CC....
12 6BKY ic50 = 270 nM K32 C7 H2 Br4 N2 O c12c(c(c(c....
13 6B0Z ic50 = 0.018 uM C81 C23 H22 F4 N6 O2 Cc1cc(ncc1....
14 6BKZ ic50 = 120 nM DWM C28 H28 F N5 O3 C[C@@H]1CN....
15 1T0L - ICT C6 H8 O7 C([C@@H]([....
16 4L03 Kd = 0.013 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
17 5SVF ic50 = 0.22 uM 70P C18 H22 N4 O2 C[C@@H](c1....
18 4KZO Kd = 0.043 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
19 6BL2 - ICT C6 H8 O7 C([C@@H]([....
70% Homology Family (30)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3INM - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 5SUN ic50 = 0.59 uM 70Q C24 H22 N4 O4 S CN(C)S(=O)....
3 6BKX - ICT C6 H8 O7 C([C@@H]([....
4 5YZH - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
5 4L06 Kd = 0.12 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
6 4UMY - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
7 6BL0 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
8 5DE1 ic50 = 46 nM 59D C28 H28 F N5 O3 C[C@@H]1CN....
9 6BL1 ic50 = 110 nM DWG C26 H24 N4 O C[C@H]1[C@....
10 5TQH ic50 = 0.02 uM 7J2 C23 H25 F N6 O2 Cc1cc(ccc1....
11 4UMX ic50 = 0.011 uM VVS C22 H30 N4 O CC(C)(C)CC....
12 6BKY ic50 = 270 nM K32 C7 H2 Br4 N2 O c12c(c(c(c....
13 6B0Z ic50 = 0.018 uM C81 C23 H22 F4 N6 O2 Cc1cc(ncc1....
14 6BKZ ic50 = 120 nM DWM C28 H28 F N5 O3 C[C@@H]1CN....
15 1T0L - ICT C6 H8 O7 C([C@@H]([....
16 4L03 Kd = 0.013 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
17 5SVF ic50 = 0.22 uM 70P C18 H22 N4 O2 C[C@@H](c1....
18 4KZO Kd = 0.043 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
19 6BL2 - ICT C6 H8 O7 C([C@@H]([....
20 2QFY - AKG C5 H6 O5 C(CC(=O)O)....
21 2QFV - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
22 4HCX - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
23 5SVN - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
24 4JA8 - 1K9 C21 H18 F3 N3 O3 S2 c1cc(cc(c1....
25 6ADI ic50 = 31.7 nM 9UO C14 H13 Cl F6 N6 C[C@H](C(F....
26 1LWD - ICT C6 H8 O7 C([C@@H]([....
27 5I95 - AKG C5 H6 O5 C(CC(=O)O)....
28 5H3E - ICT C6 H8 O7 C([C@@H]([....
29 5I96 ic50 = 100 nM 69Q C19 H17 F6 N7 O CC(C)(CNc1....
30 5SVO - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
50% Homology Family (31)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3INM - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 5SUN ic50 = 0.59 uM 70Q C24 H22 N4 O4 S CN(C)S(=O)....
3 6BKX - ICT C6 H8 O7 C([C@@H]([....
4 5YZH - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
5 4L06 Kd = 0.12 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
6 4UMY - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
7 6BL0 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
8 5DE1 ic50 = 46 nM 59D C28 H28 F N5 O3 C[C@@H]1CN....
9 6BL1 ic50 = 110 nM DWG C26 H24 N4 O C[C@H]1[C@....
10 5TQH ic50 = 0.02 uM 7J2 C23 H25 F N6 O2 Cc1cc(ccc1....
11 4UMX ic50 = 0.011 uM VVS C22 H30 N4 O CC(C)(C)CC....
12 6BKY ic50 = 270 nM K32 C7 H2 Br4 N2 O c12c(c(c(c....
13 6B0Z ic50 = 0.018 uM C81 C23 H22 F4 N6 O2 Cc1cc(ncc1....
14 6BKZ ic50 = 120 nM DWM C28 H28 F N5 O3 C[C@@H]1CN....
15 1T0L - ICT C6 H8 O7 C([C@@H]([....
16 4L03 Kd = 0.013 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
17 5SVF ic50 = 0.22 uM 70P C18 H22 N4 O2 C[C@@H](c1....
18 4KZO Kd = 0.043 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
19 6BL2 - ICT C6 H8 O7 C([C@@H]([....
20 2QFY - AKG C5 H6 O5 C(CC(=O)O)....
21 2QFV - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
22 4HCX - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
23 5SVN - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
24 4JA8 - 1K9 C21 H18 F3 N3 O3 S2 c1cc(cc(c1....
25 6ADI ic50 = 31.7 nM 9UO C14 H13 Cl F6 N6 C[C@H](C(F....
26 1LWD - ICT C6 H8 O7 C([C@@H]([....
27 5I95 - AKG C5 H6 O5 C(CC(=O)O)....
28 5H3E - ICT C6 H8 O7 C([C@@H]([....
29 5I96 ic50 = 100 nM 69Q C19 H17 F6 N7 O CC(C)(CNc1....
30 5SVO - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
31 2UXR - ICT C6 H8 O7 C([C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NAP; Similar ligands found: 123
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 NHD 0.68254 0.958904
10 NJP 0.661417 0.972973
11 NFD 0.658915 0.934211
12 NXX 0.619048 0.959459
13 DND 0.619048 0.959459
14 AMP NAD 0.606061 0.958904
15 ZID 0.605839 0.972603
16 NAQ 0.59854 0.922078
17 ATR 0.59292 0.917808
18 NAE 0.591241 0.946667
19 NDE 0.58042 0.986301
20 A22 0.571429 0.958904
21 NAJ 0.567164 0.986111
22 A2R 0.563025 0.932432
23 NDC 0.561644 0.922078
24 NA7 0.552846 0.907895
25 ODP 0.551471 0.935065
26 A2P 0.539823 0.930556
27 8ID 0.537313 0.910256
28 NPW 0.525547 0.8875
29 NZQ 0.521739 0.910256
30 CNA 0.521739 0.959459
31 NDP 0.514493 0.922078
32 PO4 PO4 A A A A PO4 0.503937 0.930556
33 1DG 0.503401 0.922078
34 DG1 0.503401 0.922078
35 TXP 0.5 0.922078
36 NMN AMP PO4 0.492958 0.921053
37 XNP 0.492958 0.875
38 25L 0.492308 0.958904
39 25A 0.492063 0.972222
40 NMN 0.486726 0.888889
41 NGD 0.485714 0.935065
42 9JJ 0.481707 0.8875
43 2AM 0.477876 0.891892
44 ADP 0.458333 0.945205
45 PAP 0.451613 0.931507
46 A2D 0.445378 0.945205
47 AN2 0.442623 0.932432
48 7L1 0.441558 0.777778
49 ADP PO3 0.44 0.944444
50 SAP 0.44 0.896104
51 AGS 0.44 0.896104
52 M33 0.439024 0.906667
53 AR6 AR6 0.438849 0.945205
54 BA3 0.438017 0.945205
55 OAD 0.43609 0.92
56 ADP BMA 0.43609 0.92
57 DQV 0.435714 0.958904
58 HEJ 0.435484 0.945205
59 ATP 0.435484 0.945205
60 OOB 0.435115 0.958904
61 B4P 0.434426 0.945205
62 AP5 0.434426 0.945205
63 GAP 0.433071 0.92
64 0WD 0.432432 0.922078
65 2A5 0.432 0.87013
66 5FA 0.432 0.945205
67 AQP 0.432 0.945205
68 AT4 0.430894 0.907895
69 00A 0.428571 0.909091
70 DAL AMP 0.427481 0.932432
71 CA0 0.427419 0.92
72 ADP ALF 0.426357 0.871795
73 ALF ADP 0.426357 0.871795
74 9X8 0.425373 0.871795
75 ACP 0.424 0.92
76 NAJ PZO 0.423841 0.897436
77 9SN 0.423358 0.897436
78 ADP VO4 0.423077 0.932432
79 VO4 ADP 0.423077 0.932432
80 WAQ 0.422222 0.884615
81 V3L 0.421875 0.945205
82 ACQ 0.421875 0.92
83 ADQ 0.421053 0.92
84 AR6 0.420635 0.918919
85 APR 0.420635 0.918919
86 ATP A A A 0.42029 0.958333
87 CO7 0.419753 0.786517
88 3OD 0.419118 0.92
89 1ZZ 0.419118 0.841463
90 DLL 0.41791 0.958904
91 AD9 0.417323 0.92
92 NAX 0.416667 0.875
93 OVE 0.416667 0.857143
94 MYR AMP 0.416058 0.841463
95 AV2 0.415385 0.868421
96 A3P 0.414634 0.944444
97 NNR 0.414414 0.72973
98 OMR 0.413793 0.831325
99 6YZ 0.412214 0.92
100 ANP 0.410853 0.92
101 A1R 0.410448 0.860759
102 ABM 0.409836 0.893333
103 A 0.408333 0.944444
104 AMP 0.408333 0.944444
105 SON 0.408 0.933333
106 PPS 0.407692 0.829268
107 5AL 0.407692 0.932432
108 NAI 0.406897 0.909091
109 7D3 0.406504 0.857143
110 ADX 0.404762 0.829268
111 ATF 0.40458 0.907895
112 3UK 0.404412 0.945946
113 TYR AMP 0.404255 0.921053
114 AMP DBH 0.404255 0.894737
115 139 0.402685 0.875
116 50T 0.401575 0.906667
117 SRP 0.401515 0.907895
118 A A 0.40146 0.972222
119 B5V 0.40146 0.933333
120 A3R 0.4 0.860759
121 3AM 0.4 0.90411
122 B5M 0.4 0.921053
123 FA5 0.4 0.933333
Ligand no: 2; Ligand: VVS; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 VVS 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4UMX; Ligand: NAP; Similar sites found with APoc: 34
This union binding pocket(no: 1) in the query (biounit: 4umx.bio1) has 275 residues
No: Leader PDB Ligand Sequence Similarity
1 1PIG BGC 1.64706
2 4UA3 COA 2.06186
3 4GCZ FMN 2.33766
4 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 2.38095
5 3ZUY TCH 2.47678
6 6BR8 6OU 3.57143
7 1IIM TTP 4.10959
8 2BVE PH5 4.20168
9 1XF1 CIT 4.23529
10 4EES FMN 4.34783
11 4L4J NAG NAG BMA MAN NAG 4.52489
12 5OCQ CIT 4.91228
13 2PR5 FMN 5.30303
14 4LHD GLY 5.41176
15 5GQI CTP 5.66802
16 3GDN MXN 6.58824
17 4G86 BNT 7.04225
18 5URY PAM 7.53425
19 3KO0 TFP 7.92079
20 5SVV FMN 8.0292
21 1N9L FMN 8.25688
22 6GG9 FMN 9.25926
23 4OAS 2SW 9.375
24 4OWK NGA 9.42029
25 4OIT MAN 11.5044
26 5E5U MLT 11.7424
27 1HEX NAD 12.7536
28 3TY3 GGG 13.1148
29 4Y1P IPM 15.1335
30 4R38 RBF 17.1429
31 2D4V NAD 20.7059
32 2D4V FLC 20.7059
33 3T50 FMN 23.4375
34 5YVT NAI 26.8362
Pocket No.: 2; Query (leader) PDB : 4UMX; Ligand: NAP; Similar sites found with APoc: 5
This union binding pocket(no: 2) in the query (biounit: 4umx.bio1) has 277 residues
No: Leader PDB Ligand Sequence Similarity
1 2Z48 NGA 2.11765
2 1LSH PLD 3.44828
3 1B4P GPS 6.91244
4 6GR0 F8W 8.04598
5 5LX9 OLB 9.50704
Pocket No.: 3; Query (leader) PDB : 4UMX; Ligand: VVS; Similar sites found with APoc: 57
This union binding pocket(no: 3) in the query (biounit: 4umx.bio1) has 278 residues
No: Leader PDB Ligand Sequence Similarity
1 6CS9 PIO None
2 3IS2 FAD 1.94805
3 4UA3 COA 2.06186
4 5HCN DAO 2.29885
5 4GCZ FMN 2.33766
6 3ZUY TCH 2.47678
7 1TV5 N8E 2.58824
8 2WKQ FMN 2.58824
9 4LIK CIT 3.06122
10 5N26 73M 3.2967
11 3B6C SDN 3.4188
12 1IIM TTP 4.10959
13 3I9U DTU 4.18251
14 1XF1 CIT 4.23529
15 1DTL BEP 4.34783
16 4EES FMN 4.34783
17 2BCG GER 4.36893
18 4L4J NAG NAG BMA MAN NAG 4.52489
19 5OCQ CIT 4.91228
20 2PR5 FMN 5.30303
21 3TDC 0EU 5.41176
22 4LHD GLY 5.41176
23 4O6M C5P 5.64516
24 5GQI CTP 5.66802
25 4DDY DN6 5.70342
26 2WOR 2AN 6
27 1OFZ FUC 6.41026
28 2HHP FLC 6.82353
29 6GBV FMN 6.84932
30 4G86 BNT 7.04225
31 4HIA FMN 7.38636
32 3TTI KBI 7.52941
33 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 7.53138
34 5URY PAM 7.53425
35 4RJD TFP 7.57576
36 5SVV FMN 8.0292
37 1N9L FMN 8.25688
38 5EFW FMN 8.33333
39 2Z6C FMN 8.52713
40 6GG9 FMN 9.25926
41 4OAS 2SW 9.375
42 4OWK NGA 9.42029
43 5LX9 OLB 9.50704
44 3O01 DXC 9.74026
45 4OIT MAN 11.5044
46 5E5U MLT 11.7424
47 1HEX NAD 12.7536
48 3KPE TM3 12.8205
49 3TY3 GGG 13.1148
50 4Y1P IPM 15.1335
51 5UR6 8KM 16.0221
52 4R38 RBF 17.1429
53 2D4V NAD 20.7059
54 2D4V FLC 20.7059
55 3T50 FMN 23.4375
56 5DJU FMN 26.2295
57 5YVT NAI 26.8362
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