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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: 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
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 with APoc: 77
This union binding pocket(no: 1) in the query (biounit: 4x7g.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 43CA NPO None
2 1LOJ URI None
3 1G0N NDP 1.59363
4 1G0N PHH 1.59363
5 6GAS FAD 1.59363
6 2F5Z FAD 1.99203
7 5Y2W PGA 2.13675
8 1YQT ADP 2.39044
9 1ZDQ MSM 2.39044
10 3VYW SAM 2.39044
11 3CGB FAD 2.78884
12 5KJW 53C 2.78884
13 3CGD NAD 2.78884
14 3CGD COA 2.78884
15 3CGD FAD 2.78884
16 2IZ1 ATR 2.78884
17 5MIT NAP 2.78884
18 5MIT FAD 2.78884
19 3TW1 AHN 2.95359
20 5DYO FLU 3.18725
21 4ETZ C2E 3.18725
22 4TQK NAG 3.18725
23 4Z87 GDP 3.58566
24 4BHL ARG 3.58566
25 1G51 AMP 3.58566
26 1YID ATP 3.58566
27 4M3P HCS 3.58566
28 5VCM UDP 3.58566
29 2WHX ADP 3.58566
30 5OCG 9R5 3.7037
31 1V59 FAD 3.98406
32 3WLE NAD 3.98406
33 2Q7V FAD 3.98406
34 6FA4 D1W 4.04624
35 4GNC ASO 4.38247
36 3CL7 HYN 4.38247
37 3UOY FAD 4.38247
38 3UOY NAP 4.38247
39 2EFX NFA 4.38247
40 5OFW 9TW 4.4843
41 5L2R MLA 4.78088
42 3HQP OXL 4.78088
43 6DZN AE3 4.78088
44 5OC1 ANN 4.78088
45 5N53 8NB 5.12821
46 4M52 M52 5.17928
47 1UYY BGC BGC 5.34351
48 1NHX FTB 5.57769
49 6GAR FAD 5.57769
50 6GH9 MIX 5.57769
51 4GID 0GH 5.57769
52 3W9Z FMN 5.57769
53 3AXB FAD 5.9761
54 3AXB PRO 5.9761
55 5KOH HCA 5.9761
56 3AB1 FAD 5.9761
57 5FUI APY 6.06061
58 5LXT 7AK 6.29371
59 4CIB 7UZ 6.3745
60 1H5R THM 6.3745
61 5YJS SAL 6.77291
62 5CLO NS8 6.77966
63 4ZUL UN1 7.17131
64 4OSP 2V4 7.56972
65 2VT3 ATP 7.56972
66 5OCS CIT 8.36653
67 5YRV 5AD 8.5
68 3KLJ FAD 8.76494
69 5BUK FAD 9.56175
70 1WHT BZS 9.80392
71 1NE7 AGP 10.3586
72 5CIC 51R 10.757
73 4JDR FAD 11.9522
74 1ZQ9 SAM 12.749
75 5H86 BCO 14.2857
76 2DT5 NAD 16.1137
77 1GXS DKA 18.9873
Pocket No.: 2; Query (leader) PDB : 4X7G; Ligand: 3Y8; Similar sites found with APoc: 77
This union binding pocket(no: 2) in the query (biounit: 4x7g.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
1 3MAN BMA BMA MAN 1.19522
2 3EGI ADP 1.45631
3 2BOY BHO 1.59363
4 5F1V 3VN 1.59363
5 1RRC ADP 1.99203
6 4FL0 PLP 1.99203
7 3GD8 GOL 2.24215
8 5C9P FUC 2.39044
9 4UEC MGT 2.5641
10 2PYY GLU 2.63158
11 5CX6 CDP 2.78884
12 2CDU ADP 2.78884
13 1JI0 ATP 2.91667
14 4QM7 GTP 2.92398
15 1NE6 SP1 3.18725
16 4CCK OGA 3.18725
17 3T7S SAM 3.18725
18 4ZV1 ARG 3.43348
19 2AWN ADP 3.58566
20 2YJP CYS 3.58566
21 1T9D 1MM 3.58566
22 5KHD C2E 3.58566
23 2WHX ADP 3.58566
24 3LRE ADP 3.58566
25 6BSW UDP 3.58566
26 6BK3 UDP 3.58566
27 5KZD RCJ 3.58566
28 2OG2 MLI 3.98406
29 3B9Q MLI 3.98406
30 3BY9 SIN 3.98406
31 5IWQ PLP 3.98406
32 4XCP PLM 4.11765
33 5KK4 44E 4.16667
34 4WZ6 ATP 4.38247
35 1JJ7 ADP 4.38247
36 5HZ9 5M8 4.44444
37 5A9A UTP 4.52675
38 1P0Z FLC 4.58015
39 2CYC TYR 4.78088
40 2PZE ATP 4.80349
41 2W97 MGO 5.06912
42 1IPC MGP 5.06912
43 2IDV M7G 5.08475
44 3VV5 SLZ 5.17928
45 6MVU K4V 5.17928
46 5BXV MGP 5.72917
47 4U00 ADP 5.7377
48 1L8B MGP 5.78947
49 1QH9 LAC 6.03448
50 5G3L SIA 6.06061
51 5G3L SIA GAL 6.06061
52 5NM7 GLY 6.77291
53 2D2F ADP 6.8
54 5TG5 JW8 6.93878
55 5GVR LMR 7.69231
56 2WMC MGP 7.86517
57 1OXV ANP 7.96813
58 1XT8 CYS 8.76494
59 1B0U ATP 9.16335
60 2CBZ ATP 9.2827
61 2W58 ADP 9.40594
62 3ITJ CIT 9.96016
63 1LSS NAD 10
64 2Y7I ARG 10.3586
65 2J5B TYE 12.3506
66 3Q2K HP7 12.749
67 2BOS GLA GAL GLC 13.2353
68 2BOS GLA GAL GLC NBU 13.2353
69 1G6H ADP 13.5458
70 5Y4R C2E 13.5458
71 5T46 MGP 13.6364
72 3UBQ SIA GAL 13.9442
73 2IDO TMP 14.4578
74 1GOJ ADP 15.1394
75 5OQW A4E 17.3228
76 3GCM 5GP 19.5122
77 1EJH M7G 37.5
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