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Receptor
PDB id Resolution Class Description Source Keywords
2V3V 1.99 Å EC: 1.7.99.4 A NEW CATALYTIC MECHANISM OF PERIPLASMIC NITRATE REDUCTASE FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 FROM C RYSTALLOGRAPHIC AND EPR DATA AND BASED ON DETAILED AN ALYSIS OF THE SIXTH LIGAND DESULFOVIBRIO DESULFURICANS NITRATE ASSIMILATION NITROGENOUS ACCEPTOR ELECTRON TRANSPODISSIMILATORY NITRATE REDUCTASE MOLYBDOPTERIN COFACTOR SULIGAND OXIDOREDUCTASE
Ref.: PERIPLASMIC NITRATE REDUCTASE REVISITED: A SULFUR A COMPLETES THE SIXTH COORDINATION OF THE CATALYTIC MOLYBDENUM. J.BIOL.INORG.CHEM. V. 13 737 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
LCP A:814;
A:815;
A:816;
A:817;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
99.451 Cl O4 [O-]C...
MGD A:811;
A:812;
Valid;
Valid;
none;
none;
submit data
740.557 C20 H26 N10 O13 P2 S2 c1nc2...
MO A:810;
Part of Protein;
none;
submit data
95.94 Mo [Mo]
SF4 A:800;
Part of Protein;
none;
submit data
351.64 Fe4 S4 [S]12...
UNX A:813;
Invalid;
none;
submit data
n/a X *
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2V3V 1.99 Å EC: 1.7.99.4 A NEW CATALYTIC MECHANISM OF PERIPLASMIC NITRATE REDUCTASE FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 FROM C RYSTALLOGRAPHIC AND EPR DATA AND BASED ON DETAILED AN ALYSIS OF THE SIXTH LIGAND DESULFOVIBRIO DESULFURICANS NITRATE ASSIMILATION NITROGENOUS ACCEPTOR ELECTRON TRANSPODISSIMILATORY NITRATE REDUCTASE MOLYBDOPTERIN COFACTOR SULIGAND OXIDOREDUCTASE
Ref.: PERIPLASMIC NITRATE REDUCTASE REVISITED: A SULFUR A COMPLETES THE SIXTH COORDINATION OF THE CATALYTIC MOLYBDENUM. J.BIOL.INORG.CHEM. V. 13 737 2008
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2JIR - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
2 2NAP - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
3 2JIP - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
4 2JIQ - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
5 2V45 - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
6 2JIO - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
7 2JIM - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
8 2V3V - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2JIR - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
2 2NAP - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
3 2JIP - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
4 2JIQ - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
5 2V45 - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
6 2JIO - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
7 2JIM - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
8 2V3V - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2JIR - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
2 2NAP - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
3 2JIP - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
4 2JIQ - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
5 2V45 - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
6 2JIO - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
7 2JIM - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
8 2V3V - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
9 2NYA - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MGD; Similar ligands found: 79
No: Ligand ECFP6 Tc MDL keys Tc
1 MGD 1 1
2 PGD O 0.706349 0.954023
3 2MD 0.694215 1
4 G1R 0.636364 0.880952
5 GP3 0.635514 0.892857
6 GNH 0.623853 0.880952
7 GSP 0.616071 0.894118
8 GDP 0.614679 0.891566
9 GTP 0.612613 0.891566
10 PGD 0.606061 0.963855
11 GCP 0.59292 0.870588
12 G2R 0.589744 0.860465
13 9GM 0.587719 0.870588
14 GNP 0.587719 0.870588
15 GMV 0.584071 0.870588
16 Y9Z 0.578512 0.813187
17 G 0.568807 0.879518
18 5GP 0.568807 0.879518
19 GFB 0.560976 0.882353
20 GDR 0.560976 0.882353
21 G3A 0.556452 0.892857
22 GDD 0.552846 0.882353
23 GKE 0.552846 0.882353
24 GDC 0.552846 0.882353
25 G5P 0.552 0.892857
26 GAV 0.550847 0.904762
27 GTG 0.548387 0.862069
28 GKD 0.547619 0.882353
29 MD1 0.547445 0.97619
30 6CK 0.544 0.862069
31 GP2 0.54386 0.860465
32 NGD 0.541985 0.882353
33 MTE 0.541284 0.855422
34 JB2 0.535433 0.882353
35 G2P 0.533898 0.860465
36 GPG 0.532787 0.882353
37 YGP 0.532258 0.895349
38 GDX 0.53125 0.892857
39 GPD 0.53125 0.852273
40 JB3 0.522727 0.872093
41 FEG 0.518797 0.813187
42 ALF 5GP 0.516949 0.8
43 ZGP 0.514925 0.844444
44 CAG 0.507246 0.815217
45 GDP AF3 0.504065 0.8
46 GDP ALF 0.504065 0.8
47 ALF GDP 0.504065 0.8
48 PTE 0.503937 0.827586
49 G G 0.5 0.870588
50 U2G 0.496296 0.905882
51 G3D 0.495868 0.879518
52 0O2 0.484127 0.879518
53 CG2 0.478261 0.905882
54 TPG 0.475862 0.879121
55 G4P 0.475806 0.879518
56 GDP 7MG 0.469697 0.83908
57 GMP 0.46789 0.785714
58 DBG 0.465753 0.872093
59 3GP 0.456897 0.845238
60 FE9 0.455172 0.852632
61 G1R G1R 0.445946 0.850575
62 G1G 0.438356 0.852273
63 G4M 0.435897 0.815217
64 GCP G 0.435115 0.823529
65 GH3 0.433071 0.869048
66 G A A A 0.430556 0.848837
67 A G 0.430556 0.858824
68 U A G G 0.427586 0.858824
69 R5I 0.424 0.845238
70 R7I 0.424 0.845238
71 DGT 0.417323 0.827586
72 GPX 0.415385 0.845238
73 2GP 0.408333 0.857143
74 DGI 0.408 0.827586
75 IDP 0.403226 0.86747
76 AKW 0.402778 0.863636
77 BGO 0.402778 0.850575
78 P2G 0.401639 0.790698
79 G U 0.4 0.872093
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2V3V; Ligand: MGD; Similar sites found with APoc: 247
This union binding pocket(no: 1) in the query (biounit: 2v3v.bio1) has 69 residues
No: Leader PDB Ligand Sequence Similarity
1 6B79 ORA None
2 1X87 NAD 1.08893
3 2Q28 ADP 1.24113
4 3EYA FAD 1.45719
5 4A59 AMP 1.473
6 1FP2 SAH 1.70455
7 4CCN OGA 1.71306
8 1DAR GDP 1.73661
9 2JHP SAH 1.86335
10 6ECT SAM 1.86916
11 2IZ1 ATR 1.89873
12 3SSO SAH 1.90931
13 5E9W SAH 1.92308
14 1G7S GDP 1.93638
15 1KBJ FMN 1.94175
16 2G7C GLA GAL NAG 1.96078
17 1SC6 NAD 1.9802
18 2AOT SAH 2.05479
19 1JQD HSM 2.05479
20 1JQD SAH 2.05479
21 3ZUY TCH 2.16718
22 3GWZ SAH 2.16802
23 5X62 SAH 2.21675
24 5BW4 SAM 2.24719
25 1F4G TP4 2.27273
26 6C5B SAH 2.34604
27 5WKC FAD 2.36337
28 1T9D FAD 2.36337
29 1KPG SAH 2.43902
30 1KPH SAH 2.43902
31 3WYA GDP 2.53456
32 4D79 ATP 2.53623
33 3MAG SAH 2.60586
34 4PNE SAH 2.64901
35 5JE8 NAD 2.64901
36 3MCT SAH 2.6936
37 1V6A TRE 2.71084
38 4R6W SAH 2.71318
39 3H8V ATP 2.73973
40 3OFK SAH 2.77778
41 1TPY SAH 2.78746
42 4N4J HG1 2.8
43 3OA2 NAD 2.83019
44 3QPB URA 2.83688
45 5L95 AMP 2.86738
46 1KZL CRM 2.88462
47 5F8F SFG 2.91777
48 2QQF A1R 2.92208
49 2OD9 A1R NCA 2.92208
50 3A23 GAL 2.9316
51 1XDS SAM 2.94118
52 1RJW ETF 2.94985
53 1SZD APR 3.0303
54 5GM1 SAH 3.0303
55 1ZEM NAD 3.05344
56 2OG7 AHB 3.08123
57 2FK8 SAM 3.14465
58 3A3B FMN 3.15789
59 6ECU SAH 3.16456
60 2R0D 4IP 3.17003
61 4ZON 4Q1 3.20513
62 3DXY SAM 3.21101
63 3G89 SAM 3.21285
64 3PNA CMP 3.24675
65 3TKY SAH 3.26087
66 6EQS BV8 3.27273
67 3RIY NAD 3.2967
68 3BXO SAM 3.34728
69 4FZV SAM 3.34728
70 4A6D SAM 3.39943
71 5M58 SAH 3.47826
72 3MB5 SAM 3.52941
73 3P2E SAH 3.55556
74 3LN9 FLC 3.59712
75 4CSD MFU 3.73444
76 5E1M PRO PRO LYS ARG ILE ALA 3.73444
77 5E1M SAH 3.73444
78 2PT9 S4M 3.73832
79 1LQY BB2 3.80435
80 4G6I RS3 3.80952
81 1S7N COA 3.84615
82 2X2T GAL NGA 3.92157
83 1BW9 NAD 3.93258
84 5D3U TRP 3.98126
85 2PS1 ORO 3.9823
86 4LEB THR THR THR THR THR THR THR 4
87 3VSE SAH 4.0201
88 4YAC NAI 4.0404
89 3FUU ADN 4.05904
90 4JE7 BB2 4.06091
91 4BUZ NAD 4.06504
92 1YC5 NCA 4.06504
93 4BUZ OAD 4.06504
94 4BUZ OCZ 4.06504
95 1VJT NAD 4.14079
96 1L7E NAI 4.16667
97 1F8G NAD 4.16667
98 5MGZ SAH 4.23729
99 3NIP 16D 4.29448
100 6HOY AR6 4.30464
101 6HOY TSN 4.30464
102 1DQN IMU 4.34783
103 5F2K OCA 4.34783
104 5F2K SAH 4.34783
105 3ORF NAD 4.38247
106 3ZG6 APR 4.39189
107 1LVL NAD 4.56432
108 2VT3 ATP 4.65116
109 4OBW SAM 4.66926
110 1MZV AMP 4.68085
111 1G55 SAH 4.70263
112 1RJD SAM 4.79042
113 5O0X FAD 4.811
114 3U6B GDP 4.82234
115 4PIO SAH 4.95356
116 4PIO AVI 4.95356
117 4PTN GXV 4.95627
118 3U31 NAD 5.17241
119 3M6P BB2 5.18135
120 3T7S SAM 5.22388
121 5D4V SAH 5.22388
122 2WBV SIA 5.29101
123 5XNC MTA 5.39084
124 2FKA BEF 5.42636
125 3G5K BB2 5.46448
126 3FGZ BEF 5.46875
127 2NXE SAM 5.51181
128 1F6B GDP 5.55556
129 2D5A COA 5.55556
130 1NV8 SAM 5.6338
131 5N53 8NB 5.64103
132 4KRI SAH 5.77367
133 6ACS CIT 5.81395
134 1XTP SAI 5.90551
135 1M2K APR 5.94744
136 1X14 NAD 5.98504
137 2IXB NAD 6.08108
138 4L2I FAD 6.08365
139 4GGZ BTN 6.08696
140 5WP4 SAH 6.10998
141 1IM8 SAI 6.14754
142 2ZX2 RAM 6.15385
143 3AB4 THR 6.17978
144 2DTJ THR 6.17978
145 1UPF URF 6.25
146 5KOK SAH 6.29723
147 3A25 SAM 6.31229
148 5WP5 SAH 6.31365
149 1RL4 BRR 6.38298
150 1WS1 BB2 6.41026
151 2J9L ATP 6.48649
152 1Q0S SAH 6.56371
153 4JLS 3ZE 6.57895
154 1L1E SAH 6.62021
155 3EW2 BTN 6.66667
156 5EPQ OLA 6.70732
157 1ZBQ NAD 6.72783
158 1YKD CMP 6.78392
159 1YBH FAD 6.94915
160 3U40 ADN 7.02479
161 6BYF CIT 7.05882
162 6GKV SAH 7.12251
163 1LSS NAD 7.14286
164 5LNW HG3 7.27848
165 5LNW RP5 7.27848
166 5Z75 NAD 7.33945
167 3GP3 SEP 7.393
168 3GRU AMP 7.45763
169 2J0B UDP 7.5
170 4RDH AMP 7.63889
171 4RDI ATP 7.63889
172 2JBM SRT 7.69231
173 1O5O U5P 7.69231
174 2YY7 NAD 7.69231
175 3TY5 ATP 7.74818
176 1D1T NAD 7.7748
177 4DR9 BB2 7.8125
178 1A5Z NAD 7.83699
179 1OBB NAD 7.91667
180 2HCJ GDP 8.10811
181 3F5A SIA GAL NAG 8.13008
182 4QTU SAM 8.14815
183 3A72 AHR AHR 8.16901
184 1QAN SAH 8.19672
185 1DJL NAP 8.21256
186 1XK5 TPG 8.33333
187 6DUB SAH 8.55856
188 1UP7 NAD 8.63309
189 4KIB SAH 8.68347
190 1XTT U5P 8.7963
191 5T85 44G 8.83721
192 5Y8L NAD 9.15254
193 1D4O NAP 9.23913
194 1Y8Q ATP 9.24856
195 4M73 M72 9.79228
196 1ZQ9 SAM 10.1754
197 1GZ6 NAI 10.3448
198 1Z0N BCD 10.4167
199 1KUJ MMA 10.5263
200 1WS5 MMA 10.5263
201 1UGW GAL 10.5263
202 1JAC AMG 10.5263
203 5A3B APR 10.5611
204 4I5I NAD 10.8014
205 1GPM AMP 10.8571
206 1PNO NAP 11.1111
207 5OJ7 AR6 11.1888
208 2OOR TXP 11.4943
209 2OOR NAD 11.4943
210 4YDD MD1 11.6183
211 4YDD MGD 11.6183
212 5CLO NS8 11.8644
213 1FQK ALF 12
214 5T67 SAH 12.0192
215 5T67 JHZ 12.0192
216 6F7X MFU 12.2222
217 4IF4 BEF 12.5
218 1KYQ NAD 12.7737
219 2IVF MGD 13.278
220 2IVF MD1 13.278
221 5JE0 AZ8 14.5749
222 5JE0 SAH 14.5749
223 6F5Z SAH 14.7541
224 1OYJ GSH 15.1515
225 1S7G NAD 15.415
226 1S7G APR 15.415
227 1KK1 GNP 15.6098
228 3BY9 SIN 16.5385
229 1G27 BB1 16.6667
230 5YF1 SFG 17.9558
231 5YF1 8V0 17.9558
232 5YZC NAG 20.2128
233 6CZ7 MGD 20.6086
234 4II2 ATP 21.6867
235 4KXQ APR 23.3333
236 1KQF MGD 29.8755
237 1H0H MGD 32.3651
238 1H0H 2MD 32.3651
239 1TMO 2MD 34.5781
240 1JOT GAL A2G 35
241 1G8K MGD 37.0678
242 2VPY MGD 37.621
243 1EU1 MGD 38.1743
244 2E7Z MGD 38.4509
245 1DMR PGD 42.8769
246 2IV2 MGD 48.6713
247 2IV2 2MD 48.6713
Pocket No.: 2; Query (leader) PDB : 2V3V; Ligand: MGD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2v3v.bio1) has 69 residues
No: Leader PDB Ligand Sequence Similarity
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