-->
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 318 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 280 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 187 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: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 SSN 1 1
2 SIN 0.473684 0.866667
3 3OH 0.428571 0.631579
4 GUA 0.409091 0.764706
5 BUA 0.409091 0.6875
6 0L1 0.409091 0.722222
Ligand no: 2; 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 : 3VZ3; Ligand: SSN; Similar sites found with APoc: 152
This union binding pocket(no: 1) in the query (biounit: 3vz3.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
1 6B79 ORA None
2 4CIB 7UZ 1.0989
3 4R84 CSF 1.53173
4 2ZWI C5P 1.60858
5 1KAE NAD 1.6129
6 2HYQ MAN MAN 1.63934
7 3RK0 AMP 1.68776
8 1EU1 GLC 1.75055
9 3NIP 16D 1.84049
10 2P3I MNA 1.86335
11 5IFK HPA 1.92308
12 1OFL NGK GCD 1.96937
13 4XFR CIT 1.96937
14 2ZBA ZBA 1.96937
15 6BSW UDP 2.07101
16 2AEB ABH 2.17391
17 4ZTD ALA GLY ALA GLY ALA 2.37154
18 1VHW ADN 2.37154
19 5L2R MLA 2.407
20 2VL1 GLY GLY 2.407
21 1YFS ALA 2.407
22 5EXK MET 2.41692
23 3F5A SIA GAL NAG 2.43902
24 3U40 ADN 2.47934
25 3BRE C2E 2.51397
26 5XK9 DMA 2.58621
27 2BHZ MAL 2.62582
28 4XFM THE 2.62582
29 5BRP PNG 2.62582
30 1Y7P RIP 2.69058
31 4DFU QUE 2.79503
32 3UYW TAU 2.80374
33 4ZH7 FUC GAL NAG GAL FUC 2.84464
34 2OEM 1AE 2.90557
35 6AZQ C5J 3.05344
36 2FKA BEF 3.10078
37 5F6U 5VK 3.18471
38 1GPM CIT 3.28228
39 2Z4T C5P 3.28228
40 5JE8 NAD 3.31126
41 4NTX AMR 3.33333
42 4M8D 23J 3.42205
43 2X1L ADN 3.43511
44 1KYQ NAD 3.64964
45 1F9V ADP 3.71991
46 5Y4R C2E 3.7415
47 1LSH PLD 3.76176
48 5TC4 NAD 3.79747
49 1FLJ GSH 3.84615
50 4Q3S X7A 3.8961
51 1TZD ADP 4
52 1VAY AZA 4.18118
53 4V15 PLP 4.22164
54 5FYR INS 4.36242
55 4YJK URA 4.36508
56 1GXU 2HP 4.3956
57 5EJL C2E 4.43548
58 5DNC ASN 4.59519
59 3NZ1 3NY 4.5977
60 6FA4 D1W 4.62428
61 3QSB 743 4.64481
62 2HIM ASP 4.7486
63 2HIM ASN 4.7486
64 5KJW 53C 4.91803
65 1SES AMP 4.98812
66 3SAO DBH 5
67 5G48 1FL 5.08021
68 2IU8 PLM 5.08021
69 5YLF BGC 5.08982
70 4DA6 GA2 5.13834
71 1L5Y BEF 5.16129
72 1HYH NAD 5.17799
73 5OCG 9R5 5.29101
74 4J6O CIT 5.30303
75 3QPB URA 5.31915
76 4R8L ASP 5.45455
77 4WCX MET 5.47046
78 5ZI9 FLC 5.76923
79 1VMK GUN 5.77617
80 1RZU ADP 5.9081
81 1YBH P22 6.12691
82 3QXV MTX 6.34921
83 4IU0 ABH 6.36364
84 3ZZH NLG 6.51466
85 1C5C TK4 6.54206
86 2NU8 COA 6.59722
87 1ZQ9 SAM 6.66667
88 2YN4 39J 6.77966
89 5FUI APY 6.81818
90 3TY3 GGG 7.10383
91 1M2X MCO 7.62332
92 1RJW ETF 7.66962
93 5KHD C2E 7.69231
94 1V3S ATP 7.75862
95 1I1Q TRP 7.8125
96 2XG5 EC5 8.25688
97 2XG5 EC2 8.25688
98 6GMN F4E 8.64198
99 6GNO XDI 8.88889
100 6F9G PUT 9.34579
101 1EYQ NAR 9.45946
102 3KYF 5GP 5GP 9.52381
103 1T36 U 9.62801
104 5E65 5N6 GAL 9.63855
105 1W8S FBP 9.88593
106 5AOG IAC 10.0977
107 1Z34 2FD 10.2128
108 5YJS SAL 10.2564
109 2B99 RDL 10.2564
110 1I7M CG 10.4478
111 2BMZ XLM 11.3475
112 4RT1 C2E 12.5
113 2RI1 GLP 12.766
114 1UYY BGC BGC 12.9771
115 1ECM TSA 13.7615
116 3ACL 3F1 14.1892
117 4KBA 1QM 14.5015
118 1VC9 ATP 15.873
119 5TVF CGQ 16
120 1EZ0 NAP 22.3195
121 1XPJ TLA 26.9841
122 5TV6 PML 27.5
123 4NS3 NAD 28.0639
124 4OE4 NAD 29.7593
125 5KF6 NAD 37.4179
126 3HAZ NAD 39.6061
127 2Y5D NAP 39.6061
128 4LH0 GLV 40.4814
129 2BJK NAD 42.2319
130 4I3V NAD 42.623
131 1T90 NAD 43.5449
132 3SZB I1E 43.5449
133 5UCD NAP 43.5449
134 2G30 ALA ALA PHE 43.75
135 4I8P NAD 44.639
136 4ZUL UN1 45.0766
137 5L2M 6ZY 45.5142
138 2W8Q SIN 45.733
139 6FK3 PPI 46.1707
140 1O9J NAD 47.046
141 4PZ2 NAD 47.2648
142 6B5G CQY 47.7024
143 6B5G NAD 47.7024
144 5X5U NAD 47.9212
145 5L13 6ZE 48.14
146 2WOX NDP 48.14
147 2QE0 NAP 48.14
148 2WME NAP 48.14
149 1KY8 NAP 49.0153
150 3JZ4 NAP 49.453
151 2IMP LAC 49.8906
152 2IMP NAI 49.8906
Pocket No.: 2; Query (leader) PDB : 3VZ3; Ligand: SSN; Similar sites found with APoc: 36
This union binding pocket(no: 2) in the query (biounit: 3vz3.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
1 3BWN PMP 1.27877
2 3VU2 CEX 1.75055
3 5LQ8 GB 1.77305
4 5LB3 ADP 1.79775
5 1K0E TRP 1.98676
6 1O8B ABF 2.28311
7 5GQX GLC GLC GLC GLC 2.407
8 3WLV AZA 2.88462
9 5CC2 CKA 3.01887
10 6E1Q CFA 3.06346
11 3I7S PYR 3.08219
12 3TBK ANP 3.28228
13 3CBC DBS 3.53535
14 1SQS TLA 3.71901
15 5D4V SAH 3.73134
16 4P8O 883 3.74332
17 2RDE C2E 3.98406
18 3LGS ADE 4.11985
19 4KTP BGC 4.37637
20 3CM2 X23 4.61538
21 5NC1 NAG 4.64135
22 5AHW CMP 4.7619
23 3KYG 5GP 5GP 4.84582
24 4JGP PYR 5.06912
25 5ZA2 NXL 5.64972
26 1C1X HFA 7.32394
27 5AHO TLA 7.44048
28 5TCI MLI 7.6087
29 5KBF CMP 7.6412
30 5FAW CHT 7.87746
31 5UKL SIX 8.53392
32 1JAY F42 9.90566
33 1UKG MMA 10.3175
34 3UW4 MAA CHG PRO 0DQ 10.8696
35 3NJQ NJQ 15.0259
36 3IWD M2T 19.3548
Pocket No.: 3; Query (leader) PDB : 3VZ3; Ligand: NAP; Similar sites found with APoc: 159
This union binding pocket(no: 3) in the query (biounit: 3vz3.bio1) has 32 residues
No: Leader PDB Ligand Sequence Similarity
1 6B79 ORA None
2 5HWV MBN None
3 2BOS GLA GAL GLC NBU None
4 2BOS GLA GAL GLC None
5 4CIB 7UZ 1.0989
6 4R84 CSF 1.53173
7 5O0J 8BR 1.54525
8 2ZWI C5P 1.60858
9 1KAE NAD 1.6129
10 1NW4 IMH 1.81159
11 5IFK HPA 1.92308
12 1OFL NGK GCD 1.96937
13 4XG0 CIT 1.96937
14 4XFR CIT 1.96937
15 6BSW UDP 2.07101
16 1WLJ U5P 2.1164
17 2WPB ZZI 2.30263
18 4ZTD ALA GLY ALA GLY ALA 2.37154
19 5L2R MLA 2.407
20 2WZF BGC 2.407
21 2WDA L42 2.407
22 4WOE ADP 2.407
23 2VL1 GLY GLY 2.407
24 5EXK MET 2.41692
25 3F5A SIA GAL NAG 2.43902
26 3U40 ADN 2.47934
27 3BRE C2E 2.51397
28 5XK9 DMA 2.58621
29 4FK7 P34 2.62009
30 4XFM THE 2.62582
31 2IZ1 ATR 2.62582
32 6CS8 F9Y 2.64026
33 1Y7P RIP 2.69058
34 4DFU QUE 2.79503
35 3UYW TAU 2.80374
36 5W75 SUC 2.80612
37 4ZH7 FUC GAL NAG GAL FUC 2.84464
38 2F6U CIT 2.99145
39 3SJK LYS PRO VAL LEU ARG THR ALA 3.15789
40 5F6U 5VK 3.18471
41 2Z4T C5P 3.28228
42 2X1L ADN 3.43511
43 3CBC DBS 3.53535
44 1KYQ NAD 3.64964
45 1F9V ADP 3.71991
46 5Y4R C2E 3.7415
47 1LSH PLD 3.76176
48 5TC4 NAD 3.79747
49 3I27 SID 3.90625
50 2RDE C2E 3.98406
51 4YJK URA 4.36508
52 1VM6 NAD 4.38596
53 1J2Z SOG 4.44444
54 3ERR AMP 4.59519
55 3NZ1 3NY 4.5977
56 3CM2 X23 4.61538
57 6FA4 D1W 4.62428
58 4V3C C 4.63918
59 5NC1 NAG 4.64135
60 3QSB 743 4.64481
61 3LJU IP9 4.66321
62 5AHW CMP 4.7619
63 3KYG 5GP 5GP 4.84582
64 5KJW 53C 4.91803
65 1SES AMP 4.98812
66 3SAO DBH 5
67 4GN8 ASO 5.01672
68 2J9D ADP 5.04202
69 5G48 1FL 5.08021
70 2IU8 PLM 5.08021
71 5YLF BGC 5.08982
72 4DA6 GA2 5.13834
73 1HYH NAD 5.17799
74 5OF1 SAL 5.2381
75 5OCG 9R5 5.29101
76 3QPB URA 5.31915
77 2POC UD1 5.44959
78 4WCX MET 5.47046
79 5LJW ANP 5.4755
80 1VMK GUN 5.77617
81 1RZU ADP 5.9081
82 5MW4 5JU 5.98802
83 1RZX ACE VAL LYS GLU SER LEU VAL 6.12245
84 5DYO FLU 6.13208
85 6DXS HJ7 6.14035
86 3QXV MTX 6.34921
87 3ZZH NLG 6.51466
88 1C5C TK4 6.54206
89 2NU8 COA 6.59722
90 1ZQ9 SAM 6.66667
91 1PVS 7HP 6.73759
92 2YN4 39J 6.77966
93 5FUI APY 6.81818
94 3TY3 GGG 7.10383
95 4EHQ GBL 7.43243
96 5AHO TLA 7.44048
97 1CTU ZEB 7.48299
98 5TCI MLI 7.6087
99 1RJW ETF 7.66962
100 1V3S ATP 7.75862
101 1I1Q TRP 7.8125
102 1MQ0 BRD 7.85714
103 2XG5 EC5 8.25688
104 2XG5 EC2 8.25688
105 1U4L H1S 8.82353
106 6GNO XDI 8.88889
107 4RF7 ARG 9.19037
108 5M6N 7H9 9.32203
109 3KYF 5GP 5GP 9.52381
110 4MTI 2DX 9.56522
111 1T36 U 9.62801
112 4NTO 1PW 9.66184
113 5AOG IAC 10.0977
114 5YJS SAL 10.2564
115 1I7M CG 10.4478
116 1LOB MMA 10.4972
117 3UW4 MAA CHG PRO 0DQ 10.8696
118 2BMZ XLM 11.3475
119 3AJ6 NGA 12.5874
120 1UYY BGC BGC 12.9771
121 3DZ6 M8E 13.4328
122 4KBA 1QM 14.5015
123 3PGL RZX 15
124 3KIF GDL 15.0943
125 5TVF CGQ 16
126 5KY9 GDP 17.5
127 3RF4 FUN 18.9655
128 3HGM ATP 19.0476
129 3IWD M2T 19.3548
130 1EZ0 NAP 22.3195
131 6GMR F4K 26.3158
132 5TV6 PML 27.5
133 4NS3 NAD 28.0639
134 4OE4 NAD 29.7593
135 5KF6 NAD 37.4179
136 3HAZ NAD 39.6061
137 2Y5D NAP 39.6061
138 4LH0 GLV 40.4814
139 2BJK NAD 42.2319
140 4I3V NAD 42.623
141 1T90 NAD 43.5449
142 5UCD NAP 43.5449
143 2G30 ALA ALA PHE 43.75
144 4I8P NAD 44.639
145 4ZUL UN1 45.0766
146 5L2M 6ZY 45.5142
147 6FK3 PPI 46.1707
148 1O9J NAD 47.046
149 4PZ2 NAD 47.2648
150 6B5G CQY 47.7024
151 6B5G NAD 47.7024
152 5X5U NAD 47.9212
153 5L13 6ZE 48.14
154 2WOX NDP 48.14
155 2QE0 NAP 48.14
156 2WME NAP 48.14
157 1KY8 NAP 49.0153
158 3JZ4 NAP 49.453
159 2IMP NAI 49.8906
Pocket No.: 4; Query (leader) PDB : 3VZ3; Ligand: NAP; Similar sites found with APoc: 16
This union binding pocket(no: 4) in the query (biounit: 3vz3.bio1) has 32 residues
No: Leader PDB Ligand Sequence Similarity
1 5CLO NS8 None
2 4PTN GXV 2.91545
3 4FE2 AIR 3.13725
4 6F4W FMC 3.43348
5 5GZZ GSH 3.66972
6 4NV1 TYD 4.11523
7 3LGS ADE 4.11985
8 1YKF NAP 4.26136
9 3QPB R1P 5.31915
10 4R8L ASP 5.45455
11 3H0L ADP 6.38298
12 4URN NOV 7.55556
13 3ZF8 GDP 7.86885
14 6GMN F4E 8.64198
15 5MRH Q9Z 9.19037
16 2O66 FLC 10.3704
APoc FAQ
Feedback