Receptor
PDB id Resolution Class Description Source Keywords
3ML1 1.6 Å EC: 1.7.99.4 CRYSTAL STRUCTURE OF THE PERIPLASMIC NITRATE REDUCTASE FROM CUPRIAVIDUS NECATOR RALSTONIA EUTROPHA HETERODIMER OXIDOREDUCTASE
Ref.: THE CRYSTAL STRUCTURE OF CUPRIAVIDUS NECATOR NITRAT REDUCTASE IN OXIDIZED AND PARTIALLY REDUCED STATES J.MOL.BIOL. V. 408 932 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
7278_ A:1802;
Part of Protein;
none;
submit data n/a n/a n/a n/a
7279_ A:1802;
Invalid;
none;
submit data n/a n/a n/a n/a
HEC B:1128;
B:1129;
Part of Protein;
Part of Protein;
none;
none;
submit data
618.503 C34 H34 Fe N4 O4 CC=C1...
MGD A:1803;
A:1804;
Valid;
Valid;
none;
none;
submit data
740.557 C20 H26 N10 O13 P2 S2 c1nc2...
SF4 A:1801;
Part of Protein;
none;
submit data
351.64 Fe4 S4 [S]12...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3ML1 1.6 Å EC: 1.7.99.4 CRYSTAL STRUCTURE OF THE PERIPLASMIC NITRATE REDUCTASE FROM CUPRIAVIDUS NECATOR RALSTONIA EUTROPHA HETERODIMER OXIDOREDUCTASE
Ref.: THE CRYSTAL STRUCTURE OF CUPRIAVIDUS NECATOR NITRAT REDUCTASE IN OXIDIZED AND PARTIALLY REDUCED STATES J.MOL.BIOL. V. 408 932 2011
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3ML1 - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
2 3O5A - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3ML1 - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
2 3O5A - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3ML1 - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
2 3O5A - 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 : 3ML1; Ligand: MGD; Similar sites found: 94
This union binding pocket(no: 1) in the query (biounit: 3ml1.bio1) has 68 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3WMX NAD 0.02169 0.40092 1.95531
2 5GM1 SAH 0.02481 0.40931 2.3569
3 4MUS LY0 0.0318 0.43006 2.8436
4 4G86 BNT 0.02084 0.44212 2.96296
5 3T7S SAM 0.01252 0.43465 2.96296
6 1V59 NAD 0.02844 0.4292 2.96296
7 2PXX SAH 0.04358 0.40484 2.96296
8 5MGZ SAH 0.02136 0.42019 2.9661
9 3U31 NAD 0.00218 0.46174 3.44828
10 1KPH SAH 0.00141 0.47066 3.7037
11 1L1E SAH 0.002019 0.46676 3.7037
12 4AZT SAM 0.03098 0.41491 3.7037
13 3VSE SAH 0.02549 0.43179 4.44444
14 4KRI SAH 0.01556 0.42413 4.44444
15 1XDS SAM 0.03359 0.42198 4.44444
16 4KRG SAH 0.033 0.41633 4.44444
17 3HX3 RET 0.04376 0.41 4.44444
18 1P31 EPU 0.04492 0.40674 4.44444
19 1T9D FAD 0.004642 0.40657 4.44444
20 1K3T BRZ 0.01381 0.40125 4.45682
21 1HSL HIS 0.0474 0.42942 4.62185
22 4RDH AMP 0.01565 0.4362 4.86111
23 5A3B APR 0.01945 0.40725 4.9505
24 4D79 ATP 0.009283 0.44115 5.07246
25 5MPT SAH 0.03168 0.41442 5.18518
26 3GDH SAH 0.01753 0.41392 5.39419
27 3BKR PLM 0.02878 0.42557 5.55556
28 1TPY SAH 0.00167 0.46719 5.57491
29 5XVQ SAH 0.02132 0.4124 5.6338
30 1OBB NAD 0.02861 0.40411 5.92593
31 4Z28 BTN 0.04341 0.42249 5.97015
32 3EGI ADP 0.008634 0.47065 6.31068
33 1N2X SAM 0.02525 0.40896 6.31229
34 3TLJ SAH 0.03463 0.40251 6.43432
35 3BGD SAH 0.02549 0.40877 6.66667
36 5K7U SAM 0.03439 0.41262 7.11111
37 1XPJ TLA 0.02464 0.42615 7.14286
38 3H2B SAH 0.0221 0.41946 7.38916
39 4OBW SAM 0.0141 0.43208 7.393
40 4QTU SAM 0.006866 0.44439 7.40741
41 5F8F SFG 0.01704 0.43427 7.40741
42 1WB4 SXX 0.04508 0.42876 7.40741
43 3OFK SAH 0.04138 0.41126 7.40741
44 5IL1 SAM 0.04749 0.40551 7.54717
45 2VDV SAM 0.02888 0.42549 7.72358
46 1NV8 MEQ 0.02452 0.40065 8.09859
47 3ZVS MLI 0.04418 0.41507 8.125
48 1X14 NAD 0.03772 0.41334 8.14815
49 1PNO NAP 0.01335 0.40788 8.14815
50 4PIO AVI 0.009916 0.40709 8.14815
51 4PIO SAH 0.01109 0.40319 8.14815
52 5H2U 1N1 0.02472 0.42277 8.61423
53 3GRU AMP 0.009411 0.42897 8.88889
54 3EW2 BTN 0.04215 0.42321 8.88889
55 1Y8Q ATP 0.01307 0.41976 8.88889
56 3A4T SFG 0.03648 0.40145 8.88889
57 5XVK SAH 0.01701 0.41699 9.15493
58 3GWZ SAH 0.01798 0.43307 9.62963
59 4EYG VNL 0.04464 0.41848 9.62963
60 2OOR TXP 0.01001 0.41769 9.62963
61 2DPM SAM 0.01968 0.41655 9.85915
62 4R6W SAH 0.007541 0.414 10.3704
63 2W9S TOP 0.01487 0.45699 10.559
64 1YTM OXD 0.04139 0.42035 11.8519
65 2VT3 ATP 0.04475 0.41843 11.8519
66 2MSB NAG BMA MAN MAN MAN MAN MAN 0.04038 0.40517 12.1739
67 4YDD MGD 0.00000000001039 0.59845 12.5926
68 4YDD MD1 0.00000000001039 0.59845 12.5926
69 4FZV SAM 0.02306 0.41586 12.5926
70 4ETZ C2E 0.04452 0.42542 13.1313
71 1ZEM NAD 0.01672 0.41017 13.3333
72 5T8O 76Z 0.03968 0.40947 13.3333
73 2VPY MGD 0.00000000001753 0.61801 14.2484
74 3DXY SAM 0.03519 0.42415 14.6789
75 2ZWA SAH 0.03396 0.40525 14.8148
76 2AOT SAH 0.00971 0.44697 15.0685
77 2IVF MGD 0.000004353 0.405 15.4613
78 4YMH SAH 0.01539 0.42436 15.5556
79 5DH3 5BS 0.03478 0.40972 15.5556
80 4II2 ATP 0.007502 0.43939 15.6627
81 5THY SAH 0.02832 0.41153 16.2963
82 3EGV SAH 0.01063 0.44149 16.3265
83 5BXV MGP 0.03217 0.45263 18.1818
84 2FKA BEF 0.01259 0.46009 20
85 5FA5 MTA 0.03749 0.41637 25.9259
86 5E8J SAH 0.02073 0.43316 29.5455
87 1KQF MGD 0.0000000008618 0.46513 29.8005
88 1G8K MGD 0.00000000000001044 0.67886 34.5387
89 1DMR PGD 0.00000001941 0.5221 35.4115
90 1EU1 MGD 0.00000219 0.40701 36.4103
91 1H0H MGD 0.00000000002328 0.7356 40.6484
92 1H0H 2MD 0.00000003215 0.63925 40.6484
93 2IV2 MGD 0.0000000006752 0.67897 46.014
94 2IV2 2MD 0.000002468 0.56096 46.014
Pocket No.: 2; Query (leader) PDB : 3ML1; 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: 3ml1.bio1) has 68 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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