Receptor
PDB id Resolution Class Description Source Keywords
4X7G 1.22 Å EC: 1.3.1.54 COBK PRECORRIN-6A REDUCTASE RHODOBACTER CAPSULATUS (STRAIN ATCC BANBRC 16581 / SB1003) OXIDOREDUCTASE NADP BINDING
Ref.: CRYSTAL STRUCTURE OF COBK REVEALS STRAND-SWAPPING B ROSSMANN-FOLD DOMAINS AND MOLECULAR BASIS OF THE RE PRECORRIN PRODUCT TRAP. SCI REP V. 5 16943 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAP A:301;
Valid;
none;
submit data
743.405 C21 H28 N7 O17 P3 c1cc(...
3Y8 A:302;
Valid;
none;
submit data
912.975 C45 H60 N4 O16 CC1=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4X7G 1.22 Å EC: 1.3.1.54 COBK PRECORRIN-6A REDUCTASE RHODOBACTER CAPSULATUS (STRAIN ATCC BANBRC 16581 / SB1003) OXIDOREDUCTASE NADP BINDING
Ref.: CRYSTAL STRUCTURE OF COBK REVEALS STRAND-SWAPPING B ROSSMANN-FOLD DOMAINS AND MOLECULAR BASIS OF THE RE PRECORRIN PRODUCT TRAP. SCI REP V. 5 16943 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4X7G - 3Y8 C45 H60 N4 O16 CC1=C2[C@H....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4X7G - 3Y8 C45 H60 N4 O16 CC1=C2[C@H....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4X7G - 3Y8 C45 H60 N4 O16 CC1=C2[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: 3Y8; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 3Y8 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4X7G; Ligand: NAP; Similar sites found: 27
This union binding pocket(no: 1) in the query (biounit: 4x7g.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2F5Z FAD 0.0116 0.41633 1.99203
2 1YQT ADP 0.01975 0.40894 2.39044
3 5KJW 53C 0.0137 0.41579 2.78884
4 3TW1 AHN 0.02672 0.40299 2.95359
5 4ETZ C2E 0.01323 0.41198 3.18725
6 4BHL ARG 0.01597 0.41522 3.58566
7 4DSU BZI 0.02418 0.40419 3.7037
8 5OFW 9TW 0.01477 0.40819 4.4843
9 3HQP OXL 0.01569 0.41796 4.78088
10 3WGT FAD 0.02983 0.40033 4.78088
11 5N53 8NB 0.01634 0.41113 5.12821
12 1UYY BGC BGC 0.02203 0.40509 5.34351
13 3W9Z FMN 0.005396 0.40007 5.57769
14 5KOH HCA 0.02034 0.40652 5.9761
15 5FUI APY 0.01179 0.40906 6.06061
16 4OSP 2V4 0.006949 0.43083 7.56972
17 3GDN HBX 0.03367 0.40072 7.96813
18 3GDN FAD 0.02505 0.40072 7.96813
19 3KLJ FAD 0.01518 0.40105 8.76494
20 5BUK FAD 0.01951 0.40665 9.56175
21 1WHT BZS 0.01201 0.41906 9.80392
22 2ZQO NGA 0.01789 0.41154 10
23 1GET NAP 0.04305 0.40405 10.757
24 1GET FAD 0.04091 0.40405 10.757
25 1ZQ9 SAM 0.004401 0.41075 12.749
26 2HQM FAD 0.01633 0.40853 15.9363
27 1GXS DKA 0.004627 0.44328 18.9873
Pocket No.: 2; Query (leader) PDB : 4X7G; Ligand: 3Y8; Similar sites found: 39
This union binding pocket(no: 2) in the query (biounit: 4x7g.bio1) has 36 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3MAN BMA BMA MAN 0.0483 0.40199 1.19522
2 3EGI ADP 0.04155 0.40834 1.45631
3 2BOY BHO 0.01096 0.42689 1.59363
4 4UEC MGT 0.03333 0.40985 2.5641
5 2PYY GLU 0.008644 0.4407 2.63158
6 1JI0 ATP 0.03652 0.41141 2.91667
7 4ZV1 ARG 0.01655 0.42579 3.43348
8 2AWN ADP 0.01813 0.4334 3.58566
9 2YJP CYS 0.01556 0.43311 3.58566
10 3LRE ADP 0.04442 0.40768 3.58566
11 1JL0 PUT 0.04022 0.40145 3.58566
12 2OG2 MLI 0.003238 0.46884 3.98406
13 3B9Q MLI 0.012 0.43729 3.98406
14 3BY9 SIN 0.03186 0.41057 3.98406
15 5KK4 44E 0.006234 0.45431 4.16667
16 1JJ7 ADP 0.04213 0.41207 4.38247
17 4WZ6 ATP 0.0431 0.40951 4.38247
18 1P0Z FLC 0.0448 0.40602 4.58015
19 2CYC TYR 0.02488 0.42119 4.78088
20 2PZE ATP 0.01743 0.43183 4.80349
21 2W97 MGO 0.01866 0.42303 5.06912
22 1IPC MGP 0.02879 0.41707 5.06912
23 3VV5 SLZ 0.01841 0.41932 5.17928
24 5BXV MGP 0.03021 0.40922 5.72917
25 2Q2A ARG 0.02652 0.40749 6.3745
26 5GVR LMR 0.0007794 0.53961 7.69231
27 2WMC MGP 0.01464 0.43662 7.86517
28 2CBZ ATP 0.0394 0.41119 9.2827
29 2W58 ADP 0.04587 0.4092 9.40594
30 2Y7I ARG 0.03719 0.40344 10.3586
31 2J5B TYE 0.04451 0.40206 12.3506
32 4G4P GLN 0.03562 0.41201 12.7049
33 2BOS GLA GAL GLC 0.03217 0.41713 13.2353
34 2BOS GLA GAL GLC NBU 0.03603 0.41322 13.2353
35 1G6H ADP 0.03931 0.41348 13.5458
36 5T46 MGP 0.03718 0.40592 13.6364
37 2IDO TMP 0.04216 0.40829 14.4578
38 1GOJ ADP 0.03336 0.41638 15.1394
39 3GCM 5GP 0.006705 0.41492 19.5122
Feedback