Receptor
PDB id Resolution Class Description Source Keywords
2IVF 1.88 Å EC: 1.17.99.2 ETHYLBENZENE DEHYDROGENASE FROM AROMATOLEUM AROMATICUM AROMATOLEUM AROMATICUM ANAEROBIC HYDROCARBON DEGRADATION MOCO FE/S CLUSTER MO- BENZYME DMSO REDUCTASE FAMILY OXIDOREDUCTASE
Ref.: CRYSTAL STRUCTURE OF ETHYLBENZENE DEHYDROGENASE FRO AROMATOLEUM AROMATICUM STRUCTURE V. 14 1377 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT A:1978;
A:1983;
 Invalid;
Invalid;
 none;
none;
 submit data
59.044 C2 H3 O2 CC(=O...
F3S B:1356;
 Part of Protein;
 none;
 submit data
295.795 Fe3 S4 S1[Fe...
GOL A:1979;
A:1980;
A:1981;
A:1982;
B:1353;
B:1355;
C:1215;
C:1216;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
HEM C:1217;
 Part of Protein;
 none;
 submit data
616.487 C34 H32 Fe N4 O4 Cc1c2...
MD1 A:1987;
 Valid;
 none;
 submit data
740.557 C20 H26 N10 O13 P2 S2 c1nc2...
MES A:1977;
 Invalid;
 none;
 submit data
195.237 C6 H13 N O4 S C1COC...
MGD A:1986;
 Valid;
 none;
 submit data
740.557 C20 H26 N10 O13 P2 S2 c1nc2...
MO A:1985;
 Part of Protein;
 none;
 submit data
95.94 Mo [Mo]
PO4 B:1354;
 Invalid;
 none;
 submit data
94.971 O4 P [O-]P...
SF4 A:1984;
B:1357;
B:1358;
B:1359;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
351.64 Fe4 S4 [S]12...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2IVF 1.88 Å EC: 1.17.99.2 ETHYLBENZENE DEHYDROGENASE FROM AROMATOLEUM AROMATICUM AROMATOLEUM AROMATICUM ANAEROBIC HYDROCARBON DEGRADATION MOCO FE/S CLUSTER MO- BENZYME DMSO REDUCTASE FAMILY OXIDOREDUCTASE
Ref.: CRYSTAL STRUCTURE OF ETHYLBENZENE DEHYDROGENASE FRO AROMATOLEUM AROMATICUM STRUCTURE V. 14 1377 2006
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2IVF - MD1 C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2IVF - MD1 C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2IVF - MD1 C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MD1; Similar ligands found: 75
No: Ligand ECFP6 Tc MDL keys Tc
1 MD1 1 1
2 GP3 0.612613 0.892857
3 GDP 0.607143 0.891566
4 G1R 0.6 0.880952
5 GTP 0.591304 0.891566
6 GNH 0.587719 0.880952
7 GSP 0.581197 0.894118
8 GMV 0.577586 0.870588
9 GCP 0.57265 0.892857
10 2MD 0.571429 0.97619
11 G2R 0.570248 0.882353
12 GNP 0.567797 0.870588
13 G 0.5625 0.879518
14 5GP 0.5625 0.879518
15 Y9Z 0.56 0.833333
16 MGD 0.547445 0.97619
17 GTG 0.543307 0.862069
18 CAG 0.536232 0.815217
19 GKE 0.535433 0.882353
20 GDC 0.535433 0.882353
21 GDD 0.535433 0.882353
22 GAV 0.532787 0.904762
23 GFB 0.53125 0.882353
24 GDR 0.53125 0.882353
25 GDP MG 0.529412 0.827586
26 G3A 0.527132 0.892857
27 6CK 0.527132 0.862069
28 GDX 0.526718 0.892857
29 GP2 0.525424 0.882353
30 GDP BEF 0.525 0.808989
31 GTP MG 0.52459 0.827586
32 G5P 0.523077 0.892857
33 JB2 0.519084 0.882353
34 GKD 0.519084 0.882353
35 G2P 0.516393 0.882353
36 GPG 0.515873 0.882353
37 YGP 0.515625 0.895349
38 GPD 0.515152 0.873563
39 NGD 0.514706 0.882353
40 ALF 5GP 0.512397 0.8
41 BEF GDP 0.512195 0.8
42 GDP AF3 0.512 0.8
43 GCP G 0.508065 0.837209
44 JB3 0.507353 0.872093
45 PGD 0.5 0.940476
46 GDP ALF 0.5 0.8
47 FEG 0.492754 0.833333
48 ZGP 0.489209 0.865169
49 DBG 0.482993 0.872093
50 G3D 0.48 0.879518
51 GDP 7MG 0.477612 0.83908
52 G G 0.476923 0.858824
53 U2G 0.471429 0.905882
54 PGD O 0.469799 0.931818
55 CG2 0.464789 0.905882
56 TPG 0.463087 0.879121
57 G4P 0.460938 0.879518
58 0O2 0.458015 0.879518
59 FE9 0.452703 0.833333
60 GMP 0.451327 0.785714
61 I2C FE2 CMO CMO 0.44898 0.827957
62 G4M 0.443038 0.815217
63 GH3 0.430769 0.891566
64 BGO 0.430556 0.850575
65 3GP 0.429752 0.845238
66 G1R G1R 0.424837 0.850575
67 GPX 0.424242 0.845238
68 DGI 0.417323 0.848837
69 U A G G 0.416107 0.858824
70 DGT 0.415385 0.848837
71 IDP 0.412698 0.86747
72 GGM 0.412162 0.831461
73 G A A A 0.409396 0.848837
74 G1G 0.407895 0.852273
75 P2G 0.4 0.790698
Ligand no: 2; 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 : 2IVF; Ligand: MD1; Similar sites found: 33
This union binding pocket(no: 1) in the query (biounit: 2ivf.bio1) has 35 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5N53 8NB 0.00936 0.44401 3.58974
2 4RL4 PPV 0.01259 0.43276 3.77358
3 5AWM ANP 0.01692 0.42014 3.97727
4 4ISS TAR 0.01689 0.42796 5.11364
5 5AHO TLA 0.03252 0.41671 5.14019
6 4WXJ GLU 0.04494 0.40546 5.94796
7 4FK7 P34 0.03304 0.41288 6.11354
8 3B6R CRN 0.03844 0.41948 6.29921
9 2AJH MET 0.04647 0.41021 7.47664
10 2RC8 DSN 0.02659 0.41578 7.48299
11 2VO4 4NM 0.003552 0.45596 8.21918
12 3AB4 LYS 0.04598 0.40115 8.42697
13 3N5C GDP 0.03089 0.40662 8.64198
14 4OVZ P85 0.004879 0.4587 9.17722
15 1G8K MGD 0.0004575 0.41602 10.5263
16 4IF4 BEF 0.007774 0.44859 10.5769
17 3QH2 3NM 0.03219 0.4134 10.8597
18 3FGZ BEF 0.03412 0.40017 10.9375
19 1L5Y BEF 0.009551 0.45472 10.9677
20 5AB1 BCD TA5 HP6 MAN 0.02434 0.42151 12.1495
21 2V3V MGD 0.000004577 0.53882 13.278
22 3BU1 HSM 0.01736 0.42404 14.1892
23 2E7Z MGD 0.001402 0.40626 14.3054
24 1DMR PGD 0.000003011 0.54253 16.2819
25 1DCP HBI 0.007421 0.43832 16.3462
26 2IV2 2MD 0.000001358 0.50658 16.3636
27 2IV2 MGD 0.0006311 0.42475 16.3636
28 1H0H 2MD 0.000008087 0.50169 20.5607
29 1H0H MGD 0.001282 0.40448 20.5607
30 1TMO 2MD 0.0003064 0.42175 24.9698
31 1EU1 MGD 0.0004695 0.43067 25.7009
32 1KQF MGD 0.0000004829 0.5343 29.932
33 2NYA MGD 0.000003137 0.48263 38.8889
Pocket No.: 2; Query (leader) PDB : 2IVF; Ligand: MGD; Similar sites found: 76
This union binding pocket(no: 2) in the query (biounit: 2ivf.bio1) has 39 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1KPG SAH 0.009288 0.41013 2.78746
2 1PL6 NAD 0.01293 0.40657 3.27103
3 3VC1 SAH 0.01286 0.40121 3.52564
4 1SQS TLA 0.02022 0.42719 3.71901
5 2Q28 ADP 0.002208 0.44457 4.20561
6 1T9D PYD 0.01885 0.41802 4.20561
7 5KVA SAM 0.009801 0.4091 4.20561
8 1D4O NAP 0.003157 0.41883 4.34783
9 4PNE SAH 0.0109 0.40433 4.6729
10 2GMM MAN MAN 0.0467 0.41215 4.7619
11 3G89 SAM 0.002522 0.45784 4.81928
12 2BD0 BIO 0.03949 0.40784 4.91803
13 5MGZ SAH 0.002507 0.44206 5.08475
14 5CLO NS8 0.02362 0.42335 5.08475
15 1XDS SAM 0.03258 0.40255 5.11364
16 5AHO TLA 0.0316 0.41514 5.14019
17 3GXO SAH 0.0303 0.40414 5.14905
18 1M2K APR 0.002906 0.41756 5.22088
19 1T3D CYS 0.03588 0.41446 5.53633
20 2FK8 SAM 0.007808 0.41642 5.60748
21 4AZT SAM 0.0112 0.41545 5.60748
22 3OFK SAH 0.01481 0.41291 5.60748
23 4D79 ATP 0.0188 0.40491 5.7971
24 4KRI SAH 0.008363 0.41508 6.00462
25 5F8F SFG 0.00863 0.42762 6.07477
26 5GM1 SAH 0.005579 0.41692 6.07477
27 5KOK SAH 0.01703 0.40398 6.54206
28 3EGI ADP 0.01429 0.4367 6.79612
29 3UEC ALA ARG TPO LYS 0.02698 0.42232 6.84932
30 1L1E SAH 0.01092 0.41596 6.96864
31 3U31 NAD 0.001996 0.4395 7.24138
32 5JGL SAM 0.0105 0.41362 7.26644
33 5VQ4 HCA 0.02205 0.427 7.47664
34 2EG5 SAH 0.04041 0.40103 7.52688
35 5BW4 SAM 0.01506 0.41256 7.94393
36 4OBW SAM 0.02346 0.40039 8.17121
37 3LST SAH 0.03713 0.40293 8.33333
38 4X1Z FUC GAL NDG 0.03871 0.41358 8.8785
39 4RDL FUC GAL NDG FUC 0.03767 0.41496 9.41558
40 4JWH SAH 0.01045 0.40248 9.58466
41 4KXQ APR 0.01412 0.4021 10
42 1G8K MGD 0.0000002775 0.43248 10.5263
43 4IF4 BEF 0.01367 0.43755 10.5769
44 3FGZ BEF 0.003556 0.47946 10.9375
45 1L5Y BEF 0.002962 0.479 10.9677
46 4RDH AMP 0.02291 0.40694 11.6822
47 1UAY ADN 0.03472 0.40116 11.9835
48 4II2 ATP 0.01268 0.40695 12.0482
49 3FUU ADN 0.007117 0.42136 12.1771
50 4QTU SAM 0.01509 0.4064 12.5926
51 2NXE SAM 0.02107 0.40259 12.6168
52 4DVR 0LY 0.01937 0.41741 12.7358
53 2V3V MGD 0.0000005708 0.55867 13.278
54 5E8J SAH 0.02646 0.40709 13.6364
55 4JWF SAH 0.009281 0.40735 13.8249
56 1VBO MAN MAN MAN 0.04759 0.40638 14.0187
57 1VBO MAN 0.04841 0.40297 14.0187
58 2E7Z MGD 0.000003845 0.50449 14.3054
59 2BQP GLC 0.02499 0.429 14.5299
60 5MPT SAH 0.01833 0.40543 15.4206
61 3ML1 MGD 0.000004353 0.405 15.4613
62 1KYQ NAD 0.02606 0.40115 16.0584
63 1DMR PGD 0.00000239 0.53159 16.2819
64 2IV2 MGD 0.00000003534 0.55681 16.3636
65 1LES GLC FRU 0.02791 0.4265 17.1271
66 2OOR TXP 0.00635 0.40388 17.8161
67 1H0H MGD 0.0000001115 0.55544 20.5607
68 1H0H 2MD 0.001578 0.42006 20.5607
69 1TMO 2MD 0.000001053 0.51695 24.9698
70 1OFS SUC 0.02155 0.43063 25
71 1EU1 MGD 0.0000001896 0.53576 25.7009
72 1KQF MGD 0.0001462 0.45043 29.932
73 2NYA MGD 0.0002038 0.43046 38.8889
74 2FKA BEF 0.02992 0.4244 40
75 1UGY GLA BGC 0.02967 0.40737 40
76 2VPY MGD 0.000001701 0.42409 42.5641
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