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: 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
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3MBC; Ligand: NAP; Similar sites found: 34
This union binding pocket(no: 1) in the query (biounit: 3mbc.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5LJW ANP 0.004966 0.43032 1.44092
2 5EP2 AZU 0.004701 0.43257 1.5625
3 4MO4 ACP 0.01413 0.41673 1.88679
4 1ZUA TOL 0.03887 0.41196 1.89274
5 1ZUA NAP 0.03887 0.41196 1.89274
6 2J62 GSZ 0.01882 0.40879 2.0202
7 3AFH GSU 0.02107 0.40046 2.04918
8 3RG9 NDP 0.02714 0.4102 2.08333
9 3RG9 WRA 0.03018 0.4102 2.08333
10 1V9N NDP 0.04283 0.40714 2.5
11 4YNU FAD 0.01531 0.42721 2.8021
12 4YNU LGC 0.01718 0.42721 2.8021
13 5C4L SIS 0.04578 0.40945 2.80374
14 2GJP BGC GLC DAF GLC GLC GLC DAF 0.02474 0.43985 3.29897
15 4R84 CSF 0.02019 0.41271 3.37972
16 1J09 GLU 0.009641 0.40235 3.4188
17 1J09 ATP 0.009641 0.40235 3.4188
18 2D3N GLC GLC GLC GLC 0.01658 0.44024 3.50515
19 2D3N GLC GLC GLC GLC GLC GLC 0.01541 0.44024 3.50515
20 3JUK UPG 0.01915 0.41686 3.55872
21 1MZC BNE 0.02408 0.40907 4.80549
22 3UMV FAD 0.03039 0.40055 4.94071
23 3D1R FBP 0.0133 0.4154 5.04451
24 2GTE VA 0.03285 0.40349 5.64516
25 3SIG AR6 0.01472 0.40556 5.77617
26 1E3Z ACI GLD GLC ACI GLD GLC ACI GLD GLC GLC 0.013 0.44097 5.7971
27 3FGC FMN 0.01321 0.42065 5.91549
28 1HEX NAD 0.0001523 0.53478 6.95652
29 2D4V NAD 0.00009044 0.55091 6.99301
30 2QZ3 XYP XYP XYP 0.01414 0.4056 7.02703
31 1YB5 NAP 0.02014 0.42498 7.69231
32 1M48 FRG 0.01035 0.40049 11.2782
33 3BC9 G6D GLC ACI GLD GLC ACI GLD GLC BGC 0.01885 0.4277 11.5192
34 5GRF ADP 0.00479 0.44801 11.7994
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