Receptor
PDB id Resolution Class Description Source Keywords
5SUN 2.48 Å EC: 1.1.1.42 IDH1 R132H IN COMPLEX WITH IDH146 HOMO SAPIENS INHIBITOR ISOCITRATE DEHYDROGENASE NADPH OXIDOREDUCTASE
Ref.: ALLOSTERIC MUTANT IDH1 INHIBITORS REVEAL MECHANISMS MUTANT AND ISOFORM SELECTIVITY. STRUCTURE V. 25 506 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:505;
B:505;
Invalid;
Invalid;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
NDP B:501;
A:501;
Valid;
Valid;
none;
none;
submit data
745.421 C21 H30 N7 O17 P3 c1nc(...
DMS A:506;
B:506;
Invalid;
Invalid;
none;
none;
submit data
78.133 C2 H6 O S CS(=O...
SO4 A:503;
B:503;
B:504;
A:504;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
70Q A:502;
B:502;
Valid;
Valid;
none;
none;
ic50 = 0.59 uM
462.521 C24 H22 N4 O4 S CN(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 (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: NDP; Similar ligands found: 159
No: Ligand ECFP6 Tc MDL keys Tc
1 NDP 1 1
2 0WD 0.827273 1
3 NAI 0.803738 0.986842
4 NMN AMP PO4 0.794643 0.948052
5 NPW 0.692308 0.962025
6 NZQ 0.686441 0.987013
7 DG1 0.68 1
8 1DG 0.68 1
9 A2R 0.650943 0.909091
10 A22 0.64486 0.934211
11 TXP 0.644628 0.924051
12 ATR 0.640777 0.894737
13 NA7 0.636364 0.886076
14 XNP 0.620968 0.949367
15 AP0 0.598361 0.948718
16 A2P 0.598039 0.881579
17 NJP 0.574803 0.923077
18 25L 0.550847 0.934211
19 ODP 0.550388 0.936709
20 NAX 0.544 0.949367
21 25A 0.53913 0.921053
22 2AM 0.529412 0.87013
23 6V0 0.519685 0.974026
24 NAP 0.514493 0.922078
25 EAD 0.507143 0.949367
26 A2D 0.504673 0.921053
27 TXE 0.503876 0.935897
28 NA0 0.496454 0.910256
29 TXD 0.496124 0.911392
30 SAP 0.495575 0.875
31 AGS 0.495575 0.875
32 P1H 0.493056 0.925926
33 CO7 0.489796 0.791209
34 TAP 0.489362 0.864198
35 PAP 0.482456 0.907895
36 BA3 0.481818 0.921053
37 NAJ PZO 0.478261 0.924051
38 ATP 0.477876 0.921053
39 B4P 0.477477 0.921053
40 ADP 0.477477 0.921053
41 AP5 0.477477 0.921053
42 OAD 0.47541 0.897436
43 5FA 0.473684 0.921053
44 AR6 0.473684 0.896104
45 APR 0.473684 0.896104
46 AQP 0.473684 0.921053
47 AN2 0.473214 0.909091
48 3OD 0.467742 0.897436
49 50T 0.464912 0.884615
50 PO4 PO4 A A A A PO4 0.463415 0.857143
51 V3L 0.461538 0.896104
52 2A5 0.46087 0.85
53 A1R 0.459016 0.841463
54 ADQ 0.459016 0.897436
55 4AD 0.459016 0.875
56 OVE 0.458716 0.8375
57 OMR 0.458647 0.813953
58 PPS 0.457627 0.811765
59 AD9 0.456897 0.897436
60 CA0 0.45614 0.897436
61 M33 0.45614 0.884615
62 ADJ 0.455882 0.879518
63 A3P 0.455357 0.894737
64 ACP 0.452174 0.897436
65 ENP 0.451613 0.85
66 UP5 0.451128 0.948052
67 SRP 0.45 0.8625
68 ANP 0.449153 0.897436
69 ACQ 0.449153 0.897436
70 PRX 0.448276 0.82716
71 5AL 0.445378 0.884615
72 7D4 0.443478 0.8375
73 ADX 0.443478 0.811765
74 AMP 0.436364 0.894737
75 A 0.436364 0.894737
76 4TC 0.433824 0.924051
77 7D3 0.433628 0.8375
78 ETB 0.433566 0.797753
79 DCA 0.433566 0.788889
80 1ZZ 0.433071 0.802326
81 BIS 0.433071 0.864198
82 00A 0.432 0.864198
83 ATF 0.429752 0.886076
84 0T1 0.427586 0.788889
85 5SV 0.427419 0.788235
86 8QN 0.427419 0.884615
87 3AM 0.427273 0.857143
88 N01 0.426573 0.884615
89 PR8 0.425197 0.811765
90 WAQ 0.425197 0.841463
91 LAD 0.425197 0.821429
92 DTP 0.425 0.8375
93 AMO 0.424 0.886076
94 PAJ 0.424 0.843373
95 APC 0.423729 0.886076
96 UPA 0.423358 0.935897
97 48N 0.422222 0.853659
98 FYA 0.421875 0.860759
99 PTJ 0.421875 0.853659
100 CNA 0.421429 0.910256
101 PUA 0.42069 0.9125
102 NXX 0.419118 0.910256
103 DND 0.419118 0.910256
104 AV2 0.418033 0.848101
105 COA 0.417808 0.788889
106 3UK 0.417323 0.897436
107 OOB 0.416 0.909091
108 IVC 0.415584 0.78022
109 DAT 0.415254 0.8375
110 NDO 0.414966 0.897436
111 139 0.414286 0.901235
112 3AT 0.413223 0.896104
113 TAT 0.413223 0.886076
114 YLB 0.413043 0.784091
115 62F 0.4125 0.823529
116 ABM 0.412281 0.848101
117 YAP 0.412214 0.875
118 YLP 0.411765 0.784091
119 ME8 0.410853 0.802326
120 NB8 0.410853 0.853659
121 SON 0.410256 0.886076
122 DLL 0.409449 0.909091
123 AHX 0.409449 0.853659
124 COS 0.409396 0.771739
125 AMX 0.409396 0.797753
126 CAO 0.409396 0.763441
127 30N 0.409396 0.72449
128 7D5 0.409091 0.8125
129 4UW 0.408759 0.9125
130 APX 0.407692 0.841463
131 SRA 0.40708 0.85
132 CMX 0.406667 0.788889
133 SCO 0.406667 0.788889
134 TYM 0.405797 0.886076
135 COD 0.405594 0.777778
136 OXK 0.405229 0.771739
137 CA6 0.405229 0.70297
138 A12 0.405172 0.886076
139 AP2 0.405172 0.886076
140 9SN 0.40458 0.853659
141 LAQ 0.404412 0.802326
142 T5A 0.404255 0.914634
143 FAM 0.403974 0.771739
144 ACO 0.403974 0.763441
145 FCX 0.403974 0.763441
146 AMP MG 0.403509 0.825
147 VO4 ADP 0.403226 0.860759
148 ADP VO4 0.403226 0.860759
149 YLC 0.402878 0.823529
150 1VU 0.402597 0.763441
151 FA5 0.401515 0.886076
152 HAX 0.401316 0.771739
153 APU 0.4 0.923077
154 TXA 0.4 0.886076
155 A U 0.4 0.898734
156 4UU 0.4 0.948052
157 AFH 0.4 0.843373
158 CAJ 0.4 0.771739
159 AR6 AR6 0.4 0.871795
Ligand no: 2; Ligand: 70Q; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 70Q 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: 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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