Receptor
PDB id Resolution Class Description Source Keywords
4L03 2.1 Å EC: 1.1.1.42 CRYSTAL STRUCTURE ANALYSIS OF HUMAN IDH1 MUTANTS IN COMPLEX AND CA2+/ALPHA-KETOGLUTARATE HOMO SAPIENS CYTOSOLIC OXIDOREDUCTASE
Ref.: MUTANT IDH1 ENHANCES THE PRODUCTION OF 2-HYDROXYGLU DUE TO ITS KINETIC MECHANISM. BIOCHEMISTRY V. 52 4563 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA C:502;
B:502;
A:502;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
NAP A:501;
C:501;
B:501;
Valid;
Valid;
Valid;
none;
none;
none;
Kd = 0.013 uM
743.405 C21 H28 N7 O17 P3 c1cc(...
AKG C:503;
A:504;
B:503;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
146.098 C5 H6 O5 C(CC(...
EDO A:503;
Invalid;
none;
submit data
62.068 C2 H6 O2 C(CO)...
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 (11)
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 4L06 Kd = 0.12 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
4 4UMY - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
5 5DE1 ic50 = 46 nM 59D C28 H28 F N5 O3 C[C@@H]1CN....
6 5TQH ic50 = 0.02 uM 7J2 C23 H25 F N6 O2 Cc1cc(ccc1....
7 4UMX ic50 = 0.011 uM VVS C22 H30 N4 O CC(C)(C)CC....
8 1T0L - ICT C6 H8 O7 C([C@@H]([....
9 4L03 Kd = 0.013 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
10 5SVF ic50 = 0.22 uM 70P C18 H22 N4 O2 C[C@@H](c1....
11 4KZO Kd = 0.043 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
70% Homology Family (21)
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 4L06 Kd = 0.12 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
4 4UMY - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
5 5DE1 ic50 = 46 nM 59D C28 H28 F N5 O3 C[C@@H]1CN....
6 5TQH ic50 = 0.02 uM 7J2 C23 H25 F N6 O2 Cc1cc(ccc1....
7 4UMX ic50 = 0.011 uM VVS C22 H30 N4 O CC(C)(C)CC....
8 1T0L - ICT C6 H8 O7 C([C@@H]([....
9 4L03 Kd = 0.013 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
10 5SVF ic50 = 0.22 uM 70P C18 H22 N4 O2 C[C@@H](c1....
11 4KZO Kd = 0.043 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
12 2QFY - AKG C5 H6 O5 C(CC(=O)O)....
13 2QFV - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
14 4HCX - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
15 5SVN - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
16 4JA8 - 1K9 C21 H18 F3 N3 O3 S2 c1cc(cc(c1....
17 1LWD - ICT C6 H8 O7 C([C@@H]([....
18 5I95 - AKG C5 H6 O5 C(CC(=O)O)....
19 5H3E - ICT C6 H8 O7 C([C@@H]([....
20 5I96 ic50 = 100 nM 69Q C19 H17 F6 N7 O CC(C)(CNc1....
21 5SVO - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
50% Homology Family (22)
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 4L06 Kd = 0.12 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
4 4UMY - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
5 5DE1 ic50 = 46 nM 59D C28 H28 F N5 O3 C[C@@H]1CN....
6 5TQH ic50 = 0.02 uM 7J2 C23 H25 F N6 O2 Cc1cc(ccc1....
7 4UMX ic50 = 0.011 uM VVS C22 H30 N4 O CC(C)(C)CC....
8 1T0L - ICT C6 H8 O7 C([C@@H]([....
9 4L03 Kd = 0.013 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
10 5SVF ic50 = 0.22 uM 70P C18 H22 N4 O2 C[C@@H](c1....
11 4KZO Kd = 0.043 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
12 2QFY - AKG C5 H6 O5 C(CC(=O)O)....
13 2QFV - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
14 4HCX - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
15 5SVN - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
16 4JA8 - 1K9 C21 H18 F3 N3 O3 S2 c1cc(cc(c1....
17 1LWD - ICT C6 H8 O7 C([C@@H]([....
18 5I95 - AKG C5 H6 O5 C(CC(=O)O)....
19 5H3E - ICT C6 H8 O7 C([C@@H]([....
20 5I96 ic50 = 100 nM 69Q C19 H17 F6 N7 O CC(C)(CNc1....
21 5SVO - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
22 2UXR - ICT C6 H8 O7 C([C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NAP; Similar ligands found: 127
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 NAD BBN 0.525974 0.865854
31 NPW 0.525547 0.8875
32 CNA 0.521739 0.959459
33 NZQ 0.521739 0.910256
34 NAD CJ3 0.519231 0.835294
35 NDP 0.514493 0.922078
36 PO4 PO4 A A A A PO4 0.503937 0.930556
37 DG1 0.503401 0.922078
38 1DG 0.503401 0.922078
39 NAD TDB 0.5 0.696078
40 TXP 0.5 0.922078
41 NMN AMP PO4 0.492958 0.921053
42 XNP 0.492958 0.875
43 25L 0.492308 0.958904
44 25A 0.492063 0.972222
45 NAD NDT 0.490909 0.747368
46 NMN 0.486726 0.888889
47 NGD 0.485714 0.935065
48 2AM 0.477876 0.891892
49 ADP 0.458333 0.945205
50 PAP 0.451613 0.931507
51 ADP MG 0.45082 0.906667
52 BEF ADP 0.447154 0.883117
53 ADP BEF 0.447154 0.883117
54 A2D 0.445378 0.945205
55 AN2 0.442623 0.932432
56 ADP PO3 0.44 0.944444
57 SAP 0.44 0.896104
58 AGS 0.44 0.896104
59 M33 0.439024 0.906667
60 AR6 AR6 0.438849 0.945205
61 BA3 0.438017 0.945205
62 ATP MG 0.436508 0.906667
63 ADP BMA 0.43609 0.92
64 OAD 0.43609 0.92
65 ATP 0.435484 0.945205
66 OOB 0.435115 0.958904
67 B4P 0.434426 0.945205
68 AP5 0.434426 0.945205
69 GAP 0.433071 0.92
70 0WD 0.432432 0.922078
71 5FA 0.432 0.945205
72 2A5 0.432 0.87013
73 AQP 0.432 0.945205
74 00A 0.428571 0.909091
75 CA0 0.427419 0.92
76 ALF ADP 0.426357 0.871795
77 ADP ALF 0.426357 0.871795
78 ACP 0.424 0.92
79 NAJ PZO 0.423841 0.897436
80 9SN 0.423358 0.897436
81 VO4 ADP 0.423077 0.932432
82 ANP MG 0.423077 0.896104
83 ADP VO4 0.423077 0.932432
84 WAQ 0.422222 0.884615
85 ACQ 0.421875 0.92
86 V3L 0.421875 0.945205
87 ADQ 0.421053 0.92
88 AR6 0.420635 0.918919
89 APR 0.420635 0.918919
90 ATP A A A 0.42029 0.958333
91 CO7 0.419753 0.786517
92 1ZZ 0.419118 0.841463
93 3OD 0.419118 0.92
94 DLL 0.41791 0.958904
95 AD9 0.417323 0.92
96 NAX 0.416667 0.875
97 OVE 0.416667 0.857143
98 MYR AMP 0.416058 0.841463
99 AV2 0.415385 0.868421
100 A3P 0.414634 0.944444
101 NNR 0.414414 0.72973
102 ALF ADP 3PG 0.413793 0.8625
103 OMR 0.413793 0.831325
104 LA8 ALF 3PG 0.413793 0.8625
105 ANP 0.410853 0.92
106 A1R 0.410448 0.860759
107 ABM 0.409836 0.893333
108 AMP 0.408333 0.944444
109 A 0.408333 0.944444
110 SON 0.408 0.933333
111 PPS 0.407692 0.829268
112 5AL 0.407692 0.932432
113 TYR AMP 0.407143 0.933333
114 NAI 0.406897 0.909091
115 7D3 0.406504 0.857143
116 DAL AMP 0.406015 0.932432
117 ADX 0.404762 0.829268
118 ATF 0.40458 0.907895
119 3UK 0.404412 0.945946
120 AMP DBH 0.404255 0.894737
121 139 0.402685 0.875
122 AMP MG 0.401639 0.893333
123 50T 0.401575 0.906667
124 SRP 0.401515 0.907895
125 A A 0.40146 0.972222
126 FA5 0.4 0.933333
127 3AM 0.4 0.90411
Ligand no: 2; Ligand: AKG; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 AKG 1 1
2 OOG 0.5 0.947368
3 69O 0.458333 0.714286
4 2IT 0.423077 0.615385
5 SHF 0.416667 0.666667
6 3PY 0.409091 0.652174
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4UMX; Ligand: NAP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4umx.bio1) has 252 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4UMX; Ligand: NAP; Similar sites found: 7
This union binding pocket(no: 2) in the query (biounit: 4umx.bio1) has 254 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4I6H 1C8 0.005803 0.47955 2.27273
2 3SAO DBH 0.0366 0.4404 3.75
3 2BVE PH5 0.04168 0.44115 4.20168
4 3TY3 GGG 0.00006331 0.63138 13.1148
5 1QKQ MAN 0.02933 0.43854 13.3803
6 2D4V NAD 0.0000001568 0.67283 20.7059
7 2D4V FLC 0.01122 0.48316 20.7059
Pocket No.: 3; Query (leader) PDB : 4UMX; Ligand: VVS; Similar sites found: 11
This union binding pocket(no: 3) in the query (biounit: 4umx.bio1) has 256 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4UA3 COA 0.03806 0.43015 2.06186
2 4I6H 1C8 0.00667 0.4769 2.27273
3 1J78 OLA 0.04885 0.45044 3.05882
4 3B6C SDN 0.043 0.45229 3.4188
5 3SAO DBH 0.03731 0.4404 3.75
6 2BVE PH5 0.04242 0.44115 4.20168
7 3TDC 0EU 0.0007398 0.53883 5.41176
8 3TY3 GGG 0.00006521 0.63138 13.1148
9 4EJ1 FOL 0.0459 0.43382 13.2075
10 2D4V NAD 0.0000001651 0.67283 20.7059
11 2D4V FLC 0.01149 0.48316 20.7059
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