Receptor
PDB id Resolution Class Description Source Keywords
2JIO 2.2 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 IRON TRANSPORTMOLYBDENUM PERIPLASMIC DISULFIDE BOND ELECTRON TRANSPORTIRON-SULFUR IRON- SULFUR METAL-BINDING DISSIMILATORY NITREDUCTASE MOLYBDOPTERIN COFACTOR SULFIDO LIGAND 4FE-4S COXIDOREDUCTASE ELECTRON PARAMAGNETIC RESONANCE
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
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 n/a X n/a
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: 78
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 GNP 0.587719 0.870588
14 GMV 0.584071 0.870588
15 Y9Z 0.578512 0.813187
16 G 0.568807 0.879518
17 5GP 0.568807 0.879518
18 GFB 0.560976 0.882353
19 GDR 0.560976 0.882353
20 G3A 0.556452 0.892857
21 GKE 0.552846 0.882353
22 GDC 0.552846 0.882353
23 GDD 0.552846 0.882353
24 G5P 0.552 0.892857
25 GAV 0.550847 0.904762
26 GTG 0.548387 0.862069
27 GKD 0.547619 0.882353
28 MD1 0.547445 0.97619
29 6CK 0.544 0.862069
30 GP2 0.54386 0.860465
31 NGD 0.541985 0.882353
32 MTE 0.541284 0.855422
33 JB2 0.535433 0.882353
34 GDP MG 0.534483 0.827586
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 GDP BEF 0.529915 0.808989
41 BEF GDP 0.529412 0.8
42 GCP G 0.525 0.837209
43 JB3 0.522727 0.872093
44 FEG 0.518797 0.813187
45 ALF 5GP 0.516949 0.8
46 GTP MG 0.516667 0.827586
47 ZGP 0.514925 0.844444
48 CAG 0.507246 0.815217
49 GDP ALF 0.504065 0.8
50 GDP AF3 0.504065 0.8
51 PTE 0.503937 0.827586
52 U2G 0.496296 0.905882
53 G3D 0.495868 0.879518
54 G G 0.492063 0.858824
55 0O2 0.484127 0.879518
56 CG2 0.478261 0.905882
57 TPG 0.475862 0.879121
58 G4P 0.475806 0.879518
59 GDP 7MG 0.469697 0.83908
60 GMP 0.46789 0.785714
61 DBG 0.465753 0.872093
62 3GP 0.456897 0.845238
63 FE9 0.455172 0.852632
64 G1R G1R 0.445946 0.850575
65 G1G 0.438356 0.852273
66 G4M 0.435897 0.815217
67 G G U 0.433824 0.858824
68 GH3 0.433071 0.869048
69 I2C FE2 CMO CMO 0.431507 0.827957
70 G A A A 0.430556 0.848837
71 U A G G 0.427586 0.858824
72 DGT 0.417323 0.827586
73 GPX 0.415385 0.845238
74 2GP 0.408333 0.857143
75 DGI 0.408 0.827586
76 IDP 0.403226 0.86747
77 BGO 0.402778 0.850575
78 P2G 0.401639 0.790698
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2V3V; Ligand: MGD; Similar sites found: 151
This union binding pocket(no: 1) in the query (biounit: 2v3v.bio1) has 69 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1DAR GDP 0.03537 0.42801 1.73661
2 1G7S GDP 0.0413 0.42086 1.93638
3 2AOT SAH 0.0256 0.4256 2.05479
4 1JQD HSM 0.02704 0.40139 2.05479
5 1JQD SAH 0.01966 0.40128 2.05479
6 3GWZ SAH 0.04014 0.41533 2.16802
7 5X62 SAH 0.03391 0.41625 2.21675
8 5BW4 SAM 0.01239 0.43867 2.24719
9 1T9D FAD 0.00268 0.41597 2.36337
10 1KPG SAH 0.007063 0.43823 2.43902
11 1KPH SAH 0.008391 0.43469 2.43902
12 3WYA GDP 0.0498 0.41965 2.53456
13 4D79 ATP 0.01251 0.43524 2.53623
14 5JE8 NAD 0.02291 0.40681 2.64901
15 4PNE SAH 0.02936 0.40642 2.64901
16 4R6W SAH 0.009179 0.41107 2.71318
17 3H8V ATP 0.004598 0.45696 2.73973
18 3OFK SAH 0.02952 0.40869 2.77778
19 1TPY SAH 0.006927 0.43863 2.78746
20 3OA2 NAD 0.01702 0.40602 2.83019
21 5L95 AMP 0.02805 0.41488 2.86738
22 5F8F SFG 0.04696 0.41173 2.91777
23 2QQF A1R 0.002712 0.44863 2.92208
24 1XDS SAM 0.01697 0.43833 2.94118
25 1SZD APR 0.01081 0.40231 3.0303
26 5GM1 SAH 0.03951 0.40033 3.0303
27 2FK8 SAM 0.004249 0.45186 3.14465
28 3A3B FMN 0.0398 0.42874 3.15789
29 2R0D 4IP 0.04434 0.42984 3.17003
30 4ZON 4Q1 0.0332 0.41392 3.20513
31 3DXY SAM 0.01632 0.44288 3.21101
32 3G89 SAM 0.04022 0.4183 3.21285
33 3PNA CMP 0.04794 0.42409 3.24675
34 3RIY NAD 0.0008763 0.4585 3.2967
35 4FZV SAM 0.02919 0.41142 3.34728
36 3P2E SAH 0.008661 0.43697 3.55556
37 3LN9 FLC 0.02338 0.43118 3.59712
38 4G4P GLN 0.04145 0.43156 3.68852
39 5E1M SAH 0.01274 0.40133 3.73444
40 5E1M PRO PRO LYS ARG ILE ALA 0.01274 0.40133 3.73444
41 1LQY BB2 0.02852 0.42012 3.80435
42 1S7N COA 0.04791 0.40089 3.84615
43 5D3U TRP 0.03683 0.43458 3.98126
44 2PS1 ORO 0.04249 0.42711 3.9823
45 3VSE SAH 0.04003 0.4216 4.0201
46 3FUU ADN 0.01778 0.42466 4.05904
47 4JE7 BB2 0.02913 0.41679 4.06091
48 4BUZ NAD 0.005134 0.43092 4.06504
49 1YC5 NCA 0.008083 0.42232 4.06504
50 4BUZ OAD 0.00708 0.41789 4.06504
51 4BUZ OCZ 0.00772 0.41631 4.06504
52 1L7E NAI 0.02628 0.40868 4.16667
53 1F8G NAD 0.04118 0.40175 4.16667
54 5MGZ SAH 0.03204 0.41201 4.23729
55 5MF6 AR6 0.002777 0.43484 4.30464
56 5MF6 7M2 0.002777 0.43484 4.30464
57 1DQN IMU 0.02364 0.44167 4.34783
58 5F2K SAH 0.01188 0.40645 4.34783
59 5F2K OCA 0.01188 0.40645 4.34783
60 4OBW SAM 0.02701 0.41845 4.66926
61 1G55 SAH 0.03405 0.4107 4.70263
62 5O0X FAD 0.03501 0.42825 4.811
63 3U6B GDP 0.03636 0.43099 4.82234
64 4PIO SAH 0.005503 0.42245 4.95356
65 4PIO AVI 0.007418 0.41927 4.95356
66 3U31 NAD 0.0003831 0.49801 5.17241
67 4K28 NAD 0.02734 0.40555 5.20446
68 3T7S SAM 0.01627 0.42952 5.22388
69 5D4V SAH 0.03513 0.40507 5.22388
70 2WBV SIA 0.04436 0.42134 5.29101
71 2FKA BEF 0.008043 0.48231 5.42636
72 3G5K BB2 0.03302 0.4198 5.46448
73 3FGZ BEF 0.0321 0.41872 5.46875
74 2NXE SAM 0.0213 0.42364 5.51181
75 2XVM SAH 0.04923 0.41357 5.52764
76 1F6B GDP 0.0318 0.42708 5.55556
77 2D5A COA 0.03027 0.40579 5.55556
78 1NV8 SAM 0.02152 0.40368 5.6338
79 4KRI SAH 0.009579 0.43486 5.77367
80 1M2K APR 0.0007326 0.46776 5.94744
81 1X14 NAD 0.0347 0.41573 5.98504
82 4GGZ BTN 0.03082 0.42783 6.08696
83 1IM8 SAI 0.04194 0.40372 6.14754
84 3AB4 THR 0.03936 0.42902 6.17978
85 2DTJ THR 0.03953 0.4253 6.17978
86 5KOK SAH 0.02348 0.4187 6.29723
87 3A25 SAM 0.03107 0.41538 6.31229
88 1RL4 BRR 0.03161 0.43448 6.38298
89 1WS1 BB2 0.02661 0.42472 6.41026
90 1Q0S SAH 0.02697 0.40583 6.56371
91 1L1E SAH 0.005599 0.44609 6.62021
92 5EPQ OLA 0.03739 0.41695 6.70732
93 1ZBQ NAD 0.01468 0.40266 6.72783
94 1LSS NAD 0.04209 0.40365 7.14286
95 3GP3 SEP 0.03237 0.44021 7.393
96 3GRU AMP 0.01638 0.41831 7.45763
97 2J0B UDP 0.03518 0.43417 7.5
98 4RDH AMP 0.01406 0.43918 7.63889
99 4RDI ATP 0.02008 0.42494 7.63889
100 3TY5 ATP 0.04069 0.42459 7.74818
101 1D1T NAD 0.02063 0.40039 7.7748
102 4DR9 BB2 0.02973 0.42219 7.8125
103 1OBB NAD 0.009319 0.42707 7.91667
104 2HCJ GDP 0.03667 0.43078 8.10811
105 3F5A SIA GAL NAG 0.0415 0.43296 8.13008
106 4QTU SAM 0.005609 0.44928 8.14815
107 3A72 AHR AHR 0.04776 0.41134 8.16901
108 1QAN SAH 0.01743 0.41961 8.19672
109 1DJL NAP 0.006021 0.41646 8.21256
110 1XK5 TPG 0.03502 0.43913 8.33333
111 1XTT U5P 0.01634 0.43578 8.7963
112 1KDO C 0.04985 0.41035 8.81057
113 1D4O NAP 0.00179 0.45375 9.23913
114 1Y8Q ATP 0.02474 0.40757 9.24856
115 4M73 M72 0.006392 0.40747 9.79228
116 1ZQ9 SAM 0.01498 0.43132 10.1754
117 1GZ6 NAI 0.01516 0.40405 10.3448
118 1Z0N BCD 0.01592 0.45899 10.4167
119 1UGW GAL 0.03626 0.40283 10.5263
120 5A3B APR 0.0006884 0.4721 10.5611
121 4I5I NAD 0.00692 0.42526 10.8014
122 1GPM AMP 0.04688 0.42628 10.8571
123 1PNO NAP 0.004727 0.42755 11.1111
124 2OOR TXP 0.003909 0.43609 11.4943
125 2OOR NAD 0.04316 0.40077 11.4943
126 4YDD MGD 0.000000000009499 0.60108 11.6183
127 4YDD MD1 0.000000000009499 0.60108 11.6183
128 5CLO NS8 0.04448 0.42726 11.8644
129 1FQK ALF 0.03024 0.43886 12
130 4IF4 BEF 0.02172 0.43194 12.5
131 1KYQ NAD 0.03798 0.41371 12.7737
132 2IVF MGD 0.0000005708 0.55867 13.278
133 2IVF MD1 0.000004577 0.53882 13.278
134 5JE0 AZ8 0.001378 0.44752 14.5749
135 5JE0 SAH 0.001378 0.44752 14.5749
136 1KK1 GNP 0.04202 0.42739 15.6098
137 3BY9 SIN 0.03194 0.43835 16.5385
138 1G27 BB1 0.04028 0.40966 16.6667
139 4II2 ATP 0.008238 0.43802 21.6867
140 4KXQ APR 0.01274 0.42609 23.3333
141 1KQF MGD 0.0000000005651 0.6947 29.8755
142 1H0H MGD 0.000000000002983 0.77153 32.3651
143 1H0H 2MD 0.0000001934 0.60786 32.3651
144 1TMO 2MD 0.000004206 0.52935 34.5781
145 1G8K MGD 0.000000000000001332 0.71785 37.0678
146 2VPY MGD 0.00000000004599 0.60724 37.621
147 1EU1 MGD 0.00000253 0.53781 38.1743
148 2E7Z MGD 0.000002387 0.54622 38.4509
149 1DMR PGD 0.00000001771 0.52427 42.8769
150 2IV2 MGD 0.00000000001223 0.74775 48.6713
151 2IV2 2MD 0.00000106 0.57711 48.6713
Pocket No.: 2; Query (leader) PDB : 2V3V; Ligand: MGD; 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: 2v3v.bio1) has 69 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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