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Receptor
PDB id Resolution Class Description Source Keywords
4JA8 1.55 Å EC: 1.1.1.42 COMPLEX OF MITOCHONDRIAL ISOCITRATE DEHYDROGENASE R140Q MUTA AGI-6780 INHIBITOR HOMO SAPIENS PROTEIN-INHIBITOR COMPLEX METABOLIC ENZYME ONCOMETABOLITE OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR COMPLEX
Ref.: TARGETED INHIBITION OF MUTANT IDH2 IN LEUKEMIA CELL CELLULAR DIFFERENTIATION. SCIENCE V. 340 622 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NDP A:501;
B:501;
Valid;
Valid;
none;
none;
submit data
745.421 C21 H30 N7 O17 P3 c1nc(...
GOL A:506;
A:507;
A:505;
A:504;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
CA B:502;
A:503;
Part of Protein;
Part of Protein;
none;
none;
submit data
40.078 Ca [Ca+2...
1K9 A:502;
Valid;
none;
submit data
481.511 C21 H18 F3 N3 O3 S2 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6ADI 1.97 Å EC: 1.1.1.42 CRYSTAL STRUCTURES OF IDH2 R140Q IN COMPLEX WITH AG-881 HOMO SAPIENS OXIDOREDUCTASE
Ref.: CRYSTAL STRUCTURES OF PAN-IDH INHIBITOR AG-881 IN C WITH MUTANT HUMAN IDH1 AND IDH2 BIOCHEM. BIOPHYS. RES. V. 503 2912 2018 COMMUN.
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 5SVN - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 4JA8 - 1K9 C21 H18 F3 N3 O3 S2 c1cc(cc(c1....
3 6ADI ic50 = 31.7 nM 9UO C14 H13 Cl F6 N6 C[C@H](C(F....
4 1LWD - ICT C6 H8 O7 C([C@@H]([....
5 5I95 - AKG C5 H6 O5 C(CC(=O)O)....
6 5H3E - ICT C6 H8 O7 C([C@@H]([....
7 5I96 ic50 = 100 nM 69Q C19 H17 F6 N7 O CC(C)(CNc1....
8 5SVO - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
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: NDP; Similar ligands found: 172
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 1DG 0.68 1
8 DG1 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 80F 0.537879 0.914634
23 2AM 0.529412 0.87013
24 6V0 0.519685 0.974026
25 NAP 0.514493 0.922078
26 7L1 0.507143 0.763441
27 EAD 0.507143 0.949367
28 A2D 0.504673 0.921053
29 TXE 0.503876 0.935897
30 NA0 0.496454 0.910256
31 TXD 0.496124 0.911392
32 SAP 0.495575 0.875
33 AGS 0.495575 0.875
34 P1H 0.493056 0.925926
35 CO7 0.489796 0.791209
36 TAP 0.489362 0.864198
37 PAP 0.482456 0.907895
38 BA3 0.481818 0.921053
39 NAJ PZO 0.478261 0.924051
40 ATP 0.477876 0.921053
41 HEJ 0.477876 0.921053
42 B4P 0.477477 0.921053
43 AP5 0.477477 0.921053
44 ADP 0.477477 0.921053
45 OAD 0.47541 0.897436
46 AR6 0.473684 0.896104
47 AQP 0.473684 0.921053
48 5FA 0.473684 0.921053
49 APR 0.473684 0.896104
50 AN2 0.473214 0.909091
51 3OD 0.467742 0.897436
52 50T 0.464912 0.884615
53 NAJ PYZ 0.464789 0.879518
54 9X8 0.463415 0.851852
55 PO4 PO4 A A A A PO4 0.463415 0.857143
56 V3L 0.461538 0.896104
57 2A5 0.46087 0.85
58 AT4 0.460177 0.886076
59 A1R 0.459016 0.841463
60 4AD 0.459016 0.875
61 ADQ 0.459016 0.897436
62 OVE 0.458716 0.8375
63 OMR 0.458647 0.813953
64 PPS 0.457627 0.811765
65 AD9 0.456897 0.897436
66 CA0 0.45614 0.897436
67 M33 0.45614 0.884615
68 ADJ 0.455882 0.879518
69 A3P 0.455357 0.894737
70 ACP 0.452174 0.897436
71 ENP 0.451613 0.85
72 UP5 0.451128 0.948052
73 SRP 0.45 0.8625
74 ANP 0.449153 0.897436
75 ACQ 0.449153 0.897436
76 PRX 0.448276 0.82716
77 A3R 0.447154 0.841463
78 5AL 0.445378 0.884615
79 7D4 0.443478 0.8375
80 ADX 0.443478 0.811765
81 6YZ 0.438017 0.897436
82 A 0.436364 0.894737
83 AMP 0.436364 0.894737
84 4TC 0.433824 0.924051
85 7D3 0.433628 0.8375
86 DCA 0.433566 0.788889
87 ETB 0.433566 0.797753
88 BIS 0.433071 0.864198
89 1ZZ 0.433071 0.802326
90 00A 0.432 0.864198
91 ATF 0.429752 0.886076
92 DQV 0.428571 0.934211
93 0T1 0.427586 0.788889
94 5SV 0.427419 0.788235
95 8QN 0.427419 0.884615
96 3AM 0.427273 0.857143
97 N01 0.426573 0.884615
98 PR8 0.425197 0.811765
99 LAD 0.425197 0.821429
100 WAQ 0.425197 0.841463
101 DTP 0.425 0.8375
102 AMO 0.424 0.886076
103 PAJ 0.424 0.843373
104 APC 0.423729 0.886076
105 UPA 0.423358 0.935897
106 48N 0.422222 0.853659
107 FYA 0.421875 0.860759
108 PTJ 0.421875 0.853659
109 CNA 0.421429 0.910256
110 PUA 0.42069 0.9125
111 DND 0.419118 0.910256
112 NXX 0.419118 0.910256
113 AV2 0.418033 0.848101
114 COA 0.417808 0.788889
115 3UK 0.417323 0.897436
116 OOB 0.416 0.909091
117 IVC 0.415584 0.78022
118 DAT 0.415254 0.8375
119 NDO 0.414966 0.897436
120 139 0.414286 0.901235
121 B5V 0.414062 0.886076
122 T99 0.413223 0.886076
123 TAT 0.413223 0.886076
124 3AT 0.413223 0.896104
125 YLB 0.413043 0.784091
126 62F 0.4125 0.823529
127 ABM 0.412281 0.848101
128 B5M 0.412214 0.875
129 YAP 0.412214 0.875
130 YLP 0.411765 0.784091
131 NB8 0.410853 0.853659
132 ME8 0.410853 0.802326
133 SON 0.410256 0.886076
134 DLL 0.409449 0.909091
135 AHX 0.409449 0.853659
136 CAO 0.409396 0.763441
137 30N 0.409396 0.72449
138 AMX 0.409396 0.797753
139 COS 0.409396 0.771739
140 7D5 0.409091 0.8125
141 4UW 0.408759 0.9125
142 F2R 0.408451 0.825581
143 APX 0.407692 0.841463
144 SRA 0.40708 0.85
145 CMX 0.406667 0.788889
146 SCO 0.406667 0.788889
147 TYM 0.405797 0.886076
148 COD 0.405594 0.777778
149 CA6 0.405229 0.70297
150 OXK 0.405229 0.771739
151 AP2 0.405172 0.886076
152 A12 0.405172 0.886076
153 9SN 0.40458 0.853659
154 LAQ 0.404412 0.802326
155 T5A 0.404255 0.914634
156 FAM 0.403974 0.771739
157 ACO 0.403974 0.763441
158 FCX 0.403974 0.763441
159 VO4 ADP 0.403226 0.860759
160 ADP VO4 0.403226 0.860759
161 YLC 0.402878 0.823529
162 1VU 0.402597 0.763441
163 B5Y 0.401515 0.875
164 FA5 0.401515 0.886076
165 HAX 0.401316 0.771739
166 AR6 AR6 0.4 0.871795
167 CAJ 0.4 0.771739
168 AFH 0.4 0.843373
169 APU 0.4 0.923077
170 A U 0.4 0.898734
171 TXA 0.4 0.886076
172 4UU 0.4 0.948052
Ligand no: 2; Ligand: 1K9; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 1K9 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6ADI; Ligand: NDP; Similar sites found with APoc: 18
This union binding pocket(no: 1) in the query (biounit: 6adi.bio1) has 72 residues
No: Leader PDB Ligand Sequence Similarity
1 3GDN MXN 2.38663
2 5OCQ CIT 2.45614
3 5MB4 NAG 3.74065
4 5N6N SUC 6.20525
5 1L7N AF3 8.05687
6 3KP6 SAL 8.60927
7 5E5U MLT 10.0503
8 2IDO TMP 10.8434
9 4Y1P IPM 13.3531
10 1HEX NAD 13.6232
11 5J32 IPM 15.6328
12 3FLK OXL 15.9341
13 5HN6 IPM 19.83
14 3TY3 GGG 22.1311
15 5YVT NAI 23.0089
16 1A05 IPM 24.3017
17 2D4V NAD 32.2196
18 2D4V FLC 32.2196
Pocket No.: 2; Query (leader) PDB : 6ADI; Ligand: NDP; Similar sites found with APoc: 1
This union binding pocket(no: 2) in the query (biounit: 6adi.bio1) has 76 residues
No: Leader PDB Ligand Sequence Similarity
1 1ON3 DXX 2.86396
Pocket No.: 3; Query (leader) PDB : 6ADI; Ligand: 9UO; Similar sites found with APoc: 117
This union binding pocket(no: 3) in the query (biounit: 6adi.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 1NU4 MLA None
2 4WG0 CHD None
3 6BLD DXJ 1.19332
4 1O6U PLM 1.48883
5 3FXU TSU 1.63934
6 6AP8 BNY 1.85874
7 1GY8 UDP 2.01511
8 2G36 TRP 2.05882
9 4O8A 2OP 2.14797
10 5HCN DAO 2.29885
11 1J78 OLA 2.38663
12 4J25 OGA 2.62009
13 3TDC 0EU 2.6253
14 2OCI TYC 2.75591
15 3BP1 GUN 2.75862
16 2R5V HHH 2.80112
17 3HX3 RET 2.8481
18 3AQT RCO 2.85714
19 4WGF HX2 2.92683
20 2F7A BEZ 3.01724
21 3R9C ECL 3.11005
22 5N7O 69Y 3.16742
23 4IA6 EIC 3.34129
24 5EE7 5MV 3.34129
25 3B9Z CO2 3.35052
26 1GEG GLC 3.51562
27 3O01 DXC 3.57143
28 5ZIC BMA Z4Y NAG 3.57995
29 3ZQE DXC 3.60656
30 1Q3A NGH 3.63636
31 3P9T TCL 3.65297
32 5HGZ MLA 3.7037
33 1LNX URI 3.7037
34 1XMY ROL 3.76884
35 3ET1 ET1 3.81862
36 2OVD DAO 3.84615
37 6AYH C3G 3.9801
38 1SBR VIB 4
39 5W7B MYR 4.05728
40 5CDH TLA 4.05728
41 1ZED PNP 4.05728
42 3LA3 2FT 4.11523
43 3HYW DCQ 4.29594
44 6H8S FSZ 4.31894
45 6BR8 PGV 4.36508
46 6C0B PAM 4.48718
47 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 4.60251
48 6CS8 F9Y 4.62046
49 5M37 9SZ 4.78261
50 3GL0 HXX 4.87106
51 1HFE CYS 4.98812
52 1U6R IOM 5
53 3BJC WAN 5.01193
54 2Z77 NCA 5.03597
55 4QBK 3NZ 5.15464
56 6FBA D48 5.15759
57 5M36 9SZ 5.26316
58 6CAY ERG 5.32544
59 2WG9 OCA 5.38462
60 1M2Z BOG 5.44747
61 5OSW DIU 5.48926
62 5LX9 OLB 5.6338
63 5UGW GSH 5.71429
64 5UNJ RJW 5.71429
65 3SHZ 5CO 6.05187
66 4YMU ARG 6.36364
67 2VQ5 HBA 6.46766
68 1Y0L HAN 6.48148
69 2F99 AKV 6.53595
70 4JP3 CIT 6.69456
71 1VRP IOM 6.82415
72 5XQW 8EU 6.91244
73 3TKY N7I 7.06522
74 2CHT TSA 7.08661
75 4OGQ 2WD 7.26257
76 5XJD 87L 7.27273
77 6AYI C3G 7.53769
78 4K7O EKZ 7.7381
79 2Y7P SAL 7.79817
80 2BCG GER 8.11456
81 3W68 VIV 8.27068
82 4UYF 73B 8.44156
83 2UW1 GVM 8.57988
84 3KP6 SAL 8.60927
85 5N17 8FK 8.69565
86 5ZQ4 AMP 8.83055
87 1DKF OLA 8.93617
88 4INW 1EY 9.28571
89 1RV1 IMZ 9.41177
90 2VWA PTY 9.90099
91 2NZU BG6 10
92 4XCP PLM 10.0239
93 5V03 658 10.0671
94 3AQA BYH 10.1562
95 2XKO AKG 10.3604
96 2XHK AKG 10.3604
97 5C1M OLC 10.4
98 5C1M CLR 10.4
99 4RJD TFP 10.6061
100 4IN9 SER TRP PHE PRO 11.4458
101 3KXC PLM 11.8557
102 3KO0 TFP 11.8812
103 2WCJ M21 12.0567
104 5CHR 4NC 13.1387
105 3G08 FEE 14.1414
106 1T0S BML 15.1163
107 5NNT DPV 16.2162
108 3G4Q MCH 17.1233
109 2Y69 CHD 18.75
110 4IHL 1F5 22.2222
111 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 23.8095
112 5N18 8HZ 23.8532
113 5Z84 CHD 25.4237
114 5ZCO CHD 25.4237
115 5W97 CHD 25.4237
116 5ZCO PGV 25.4237
117 3STD MQ0 25.4545
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