Receptor
PDB id Resolution Class Description Source Keywords
3VZ3 1.69 Å EC: 1.-.-.- STRUCTURAL INSIGHTS INTO SUBSTRATE AND COFACTOR SELECTION BY SYNECHOCOCCUS SUBSTRATE SELECTION COFACTOR PREFERENCE OXIDOREDUCTASE
Ref.: STRUCTURAL BASIS FOR COFACTOR AND SUBSTRATE SELECTI CYANOBACTERIUM SUCCINIC SEMIALDEHYDE DEHYDROGENASE J.STRUCT.BIOL. V. 182 125 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SSN B:501;
A:501;
Valid;
Valid;
none;
none;
submit data
102.089 C4 H6 O3 C(CC(...
NAP A:502;
B:502;
Valid;
Valid;
none;
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
3VZ3 1.69 Å EC: 1.-.-.- STRUCTURAL INSIGHTS INTO SUBSTRATE AND COFACTOR SELECTION BY SYNECHOCOCCUS SUBSTRATE SELECTION COFACTOR PREFERENCE OXIDOREDUCTASE
Ref.: STRUCTURAL BASIS FOR COFACTOR AND SUBSTRATE SELECTI CYANOBACTERIUM SUCCINIC SEMIALDEHYDE DEHYDROGENASE J.STRUCT.BIOL. V. 182 125 2013
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 280 families.
1 4ITB - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 3VZ3 - 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 247 families.
1 4ITB - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 3VZ3 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 177 families.
1 4ITB - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 3VZ3 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
3 4YWV Ki = 0.1 mM SSN C4 H6 O3 C(CC(=O)O)....
4 4OHT - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
5 4YWU Ki = 0.1 mM SSN C4 H6 O3 C(CC(=O)O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SSN; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 SSN 1 1
2 0L1 0.409091 0.722222
3 GUA 0.409091 0.764706
4 BUA 0.409091 0.6875
Ligand no: 2; 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 : 3VZ3; Ligand: SSN; Similar sites found: 49
This union binding pocket(no: 1) in the query (biounit: 3vz3.bio1) has 36 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3KPE TM3 0.04564 0.40307 None
2 3NIP 16D 0.04512 0.40769 1.84049
3 5IFK HPA 0.02262 0.4256 1.92308
4 1OFL NGK GCD 0.003405 0.45873 1.96937
5 4XFR CIT 0.03731 0.41119 1.96937
6 2ZBA ZBA 0.02167 0.40845 1.96937
7 5BRP PNG 0.03909 0.40722 2.62582
8 5F6U 5VK 0.02946 0.40525 3.18471
9 2Z4T C5P 0.04191 0.40073 3.28228
10 5JE8 NAD 0.008282 0.40632 3.31126
11 5MX4 HPA 0.03165 0.41005 3.43348
12 2X1L ADN 0.0436 0.40338 3.43511
13 4Q3S X7A 0.03346 0.40236 3.8961
14 4V15 PLP 0.03201 0.40334 4.22164
15 1GXU 2HP 0.04958 0.41637 4.3956
16 5DNC ASN 0.02837 0.41337 4.59519
17 3NZ1 3NY 0.01399 0.4343 4.5977
18 1SES AMP 0.04939 0.40047 4.98812
19 4WCX MET 0.006354 0.45352 5.47046
20 1RZU ADP 0.03267 0.40289 5.9081
21 5FUI APY 0.0007708 0.48185 6.81818
22 2XG5 EC5 0.0006925 0.51542 8.25688
23 2XG5 EC2 0.0006925 0.51542 8.25688
24 1Z34 2FD 0.02709 0.40702 10.2128
25 4KBA 1QM 0.04536 0.40246 14.5015
26 5TVF CGQ 0.006057 0.43985 16
27 1EZ0 NAP 0.0000005255 0.54826 22.3195
28 4NS3 NAD 0.00000023 0.62815 28.0639
29 4OE4 NAD 0.000000003623 0.51076 29.7593
30 5KF6 NAD 0.0000000003148 0.627 37.4179
31 3HAZ NAD 0.0000000007633 0.6007 39.6061
32 2Y5D NAP 0.00000001458 0.55146 39.6061
33 4LH0 GLV 0.0000000003103 0.64771 40.4814
34 2BJK NAD 0.000000000895 0.62331 42.2319
35 4I3V NAD 0.0000000004158 0.61647 42.623
36 5UCD NAP 0.000000001516 0.67109 43.5449
37 1T90 NAD 0.0000000002343 0.62604 43.5449
38 5U0L 8YP 0.005664 0.45858 43.5449
39 4I8P NAD 0.0000000003973 0.63008 44.639
40 4ZUL UN1 0.000000003535 0.63663 45.0766
41 1O9J NAD 0.000000002817 0.58378 47.046
42 4PZ2 NAD 0.0000000001182 0.6864 47.2648
43 2QE0 NAP 0.000000001249 0.63419 48.14
44 2WOX NDP 0.000000004346 0.59928 48.14
45 5L13 6ZE 0.000000000006546 0.59265 48.14
46 2WME NAP 0.000001082 0.44342 48.14
47 1KY8 NAP 0.0000000001764 0.60586 49.0153
48 3JZ4 NAP 0.0000000002349 0.70385 49.453
49 2IMP NAI 0.00000004994 0.56882 49.8906
Pocket No.: 2; Query (leader) PDB : 3VZ3; Ligand: SSN; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3vz3.bio1) has 36 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3VZ3; Ligand: NAP; Similar sites found: 49
This union binding pocket(no: 3) in the query (biounit: 3vz3.bio1) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5IFK HPA 0.01493 0.43096 1.92308
2 1OFL NGK GCD 0.00276 0.45877 1.96937
3 4XFR CIT 0.01391 0.4333 1.96937
4 2BH9 NAP 0.0147 0.4088 1.96937
5 4XG0 CIT 0.04626 0.40183 1.96937
6 3SJK LYS PRO VAL LEU ARG THR ALA 0.01411 0.43351 3.15789
7 5F6U 5VK 0.0233 0.40745 3.18471
8 2Z4T C5P 0.03496 0.4006 3.28228
9 5MX4 HPA 0.02993 0.40687 3.43348
10 2X1L ADN 0.03899 0.40177 3.43511
11 3NZ1 3NY 0.01025 0.43733 4.5977
12 3LJU IP9 0.0236 0.41079 4.66321
13 3KYG 5GP 5GP 0.006571 0.41829 4.84582
14 1SES AMP 0.01496 0.42363 4.98812
15 2IU8 PLM 0.009643 0.40453 5.08021
16 4WCX MET 0.004919 0.45717 5.47046
17 1RZU ADP 0.02615 0.40347 5.9081
18 5MW4 5JU 0.005141 0.40241 5.98802
19 5FUI APY 0.000594 0.48508 6.81818
20 2XG5 EC5 0.0005405 0.51624 8.25688
21 2XG5 EC2 0.0005405 0.51624 8.25688
22 5M6N 7H9 0.03011 0.41344 9.32203
23 1LOB MMA 0.03019 0.40763 10.4972
24 3AJ6 NGA 0.04659 0.40608 12.5874
25 4KBA 1QM 0.03574 0.40377 14.5015
26 5TVF CGQ 0.003236 0.44857 16
27 5KY9 GDP 0.02394 0.40195 17.5
28 1EZ0 NAP 0.0000001895 0.55721 22.3195
29 4NS3 NAD 0.0000001534 0.62835 28.0639
30 4OE4 NAD 0.000000002174 0.54805 29.7593
31 5KF6 NAD 0.0000000002526 0.6667 37.4179
32 3HAZ NAD 0.0000000001575 0.66463 39.6061
33 2Y5D NAP 0.00000001736 0.57945 39.6061
34 4LH0 GLV 0.000000002424 0.63884 40.4814
35 2BJK NAD 0.00000000008865 0.68873 42.2319
36 4I3V NAD 0.00000000007691 0.68335 42.623
37 5UCD NAP 0.0000000002043 0.69647 43.5449
38 1T90 NAD 0.00000000007803 0.68312 43.5449
39 4I8P NAD 0.0000000000252 0.70675 44.639
40 4ZUL UN1 0.0000001297 0.56848 45.0766
41 1O9J NAD 0.0000000006905 0.64155 47.046
42 4PZ2 NAD 0.00000000001485 0.70991 47.2648
43 2QE0 NAP 0.00000000003618 0.7173 48.14
44 2WOX NDP 0.00000000009405 0.68776 48.14
45 5L13 6ZE 0.00000000003604 0.55237 48.14
46 2WME NAP 0.00000047 0.47841 48.14
47 1KY8 NAP 0.0000000001207 0.58836 49.0153
48 3JZ4 NAP 0.00000000003165 0.72868 49.453
49 2IMP NAI 0.0000001169 0.57483 49.8906
Pocket No.: 4; Query (leader) PDB : 3VZ3; Ligand: NAP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3vz3.bio1) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback