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Receptor
PDB id Resolution Class Description Source Keywords
3MBC 1.9 Å EC: 1.1.1.42 CRYSTAL STRUCTURE OF MONOMERIC ISOCITRATE DEHYDROGENASE FROM CORYNEBACTERIUM GLUTAMICUM IN COMPLEX WITH NADP CORYNEBACTERIUM GLUTAMICUM HOLOENZYME APOENZYME OPEN CONFORMATION NADP GLYOXYLATE BMAGNESIUM METAL-BINDING OXIDOREDUCTASE TRICARBOXYLIC ACI
Ref.: STRUCTURE OF A HIGHLY NADP+-SPECIFIC ISOCITRATE DEHYDROGENASE. ACTA CRYSTALLOGR.,SECT.D V. 67 856 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:739;
B:739;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
NAP A:740;
Valid;
none;
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
3MBC 1.9 Å EC: 1.1.1.42 CRYSTAL STRUCTURE OF MONOMERIC ISOCITRATE DEHYDROGENASE FROM CORYNEBACTERIUM GLUTAMICUM IN COMPLEX WITH NADP CORYNEBACTERIUM GLUTAMICUM HOLOENZYME APOENZYME OPEN CONFORMATION NADP GLYOXYLATE BMAGNESIUM METAL-BINDING OXIDOREDUCTASE TRICARBOXYLIC ACI
Ref.: STRUCTURE OF A HIGHLY NADP+-SPECIFIC ISOCITRATE DEHYDROGENASE. ACTA CRYSTALLOGR.,SECT.D V. 67 856 2011
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 3MBC - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3MBC - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
2 1ITW - ICT C6 H8 O7 C([C@@H]([....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3MBC - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
2 1ITW - 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
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3MBC; Ligand: NAP; Similar sites found with APoc: 69
This union binding pocket(no: 1) in the query (biounit: 3mbc.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 5LJW ANP 1.44092
2 5EP2 AZU 1.5625
3 4YSW FAD 1.673
4 4YSW NAI 1.673
5 2IVN ANP 1.81818
6 4MO4 ACP 1.88679
7 1ZUA TOL 1.89274
8 1ZUA NAP 1.89274
9 2J62 GSZ 2.0202
10 3AFH GSU 2.04918
11 3RG9 WRA 2.08333
12 3RG9 NDP 2.08333
13 2BW7 APC 2.28311
14 3WDM ADN 2.29885
15 4DOO DAO 2.43902
16 1V9N NDP 2.5
17 4XH4 PPI 2.64423
18 4XH4 ANP 2.64423
19 5BQ5 ADP BEF 2.6455
20 4YNU FAD 2.8021
21 4YNU LGC 2.8021
22 5C4L SIS 2.80374
23 4BR5 ANP 3.06346
24 2YCH ATP 3.18302
25 2X06 NAD 3.19767
26 1J0D 5PA 3.22581
27 4R84 CSF 3.37972
28 1J09 ATP 3.4188
29 1J09 GLU 3.4188
30 2D3N GLC GLC GLC GLC 3.50515
31 2D3N GLC GLC GLC GLC GLC GLC 3.50515
32 3JUK UPG 3.55872
33 4ZLU 4PW 3.57942
34 4ZLU ADP 3.57942
35 3DST GRG 3.92749
36 3ZGJ RMN 4.04313
37 1MZC FPP 4.80549
38 1MZC BNE 4.80549
39 3UMV FAD 4.94071
40 3D1R FBP 5.04451
41 5K8P 6R8 5.14905
42 6DIO NAD 5.36131
43 4D5G FAD 5.43294
44 4D5G TPP 5.43294
45 1SES AHX 5.46318
46 5EXE 5SR 5.56962
47 2GTE VA 5.64516
48 3SIG AR6 5.77617
49 1E3Z ACI GLD GLC ACI GLD GLC ACI GLD GLC GLC 5.7971
50 3FGC FMN 5.91549
51 1UCN ADP 5.92105
52 3ABI NAD 6.0274
53 3BOS CDP 6.19835
54 1TUU AMP 6.76692
55 4PTZ FMN 6.80628
56 1HEX NAD 6.95652
57 2D4V NAD 6.99301
58 3HRD MCN 7.27273
59 1YB5 NAP 7.69231
60 2UXR ICT 7.9602
61 3BF1 ADP 10.4418
62 1F3F D4T 10.9677
63 4XSH NAI 11.1732
64 1M48 FRG 11.2782
65 3BC9 G6D GLC ACI GLD GLC ACI GLD GLC BGC 11.5192
66 5YVT NAI 11.7994
67 2WAT COA 12.2951
68 2PID YSA 16.0112
69 4BQS K2Q 17.0455
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