Receptor
PDB id Resolution Class Description Source Keywords
5VE5 2.35 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF PERSULFIDE DIOXYGENASE RHODANESE FUSION WITH RHODANESE DOMAIN INACTIVATING MUTATION (C314S) FROM BUP HYTOFIRMANS IN COMPLEX WITH GLUTATHIONE PARABURKHOLDERIA PHYTOFIRMANS (STRAIN / LMG 22146 / PSJN) PERSULFIDE DIOXYGENASE RHODANESE OXIDOREDUCTASE TRANSFERA
Ref.: STRUCTURAL AND BIOCHEMICAL ANALYSES INDICATE THAT A BACTERIAL PERSULFIDE DIOXYGENASE-RHODANESE FUSION P FUNCTIONS IN SULFUR ASSIMILATION. J. BIOL. CHEM. V. 292 14026 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FE A:401;
C:401;
B:401;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
55.845 Fe [Fe+3...
CL C:403;
A:403;
B:403;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
35.453 Cl [Cl-]
GSH C:402;
A:402;
B:402;
Valid;
Valid;
Valid;
none;
none;
Atoms found LESS than expected: % Diff = 0.6;
submit data
307.323 C10 H17 N3 O6 S C(CC(...
PGE A:405;
Invalid;
none;
submit data
150.173 C6 H14 O4 C(COC...
IMD A:404;
C:404;
Invalid;
Invalid;
none;
none;
submit data
69.085 C3 H5 N2 c1c[n...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5VE5 2.35 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF PERSULFIDE DIOXYGENASE RHODANESE FUSION WITH RHODANESE DOMAIN INACTIVATING MUTATION (C314S) FROM BUP HYTOFIRMANS IN COMPLEX WITH GLUTATHIONE PARABURKHOLDERIA PHYTOFIRMANS (STRAIN / LMG 22146 / PSJN) PERSULFIDE DIOXYGENASE RHODANESE OXIDOREDUCTASE TRANSFERA
Ref.: STRUCTURAL AND BIOCHEMICAL ANALYSES INDICATE THAT A BACTERIAL PERSULFIDE DIOXYGENASE-RHODANESE FUSION P FUNCTIONS IN SULFUR ASSIMILATION. J. BIOL. CHEM. V. 292 14026 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 5VE5 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 5VE5 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 5VE5 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GSH; Similar ligands found: 50
No: Ligand ECFP6 Tc MDL keys Tc
1 GSH 1 1
2 HCG 0.75 0.973684
3 HGS 0.730769 0.925
4 GSM 0.690909 0.878049
5 GDS 0.672727 0.837209
6 GS8 0.672727 0.840909
7 GTS 0.672727 0.660714
8 GSF 0.660714 0.72549
9 AHE 0.649123 0.9
10 3GC 0.645833 0.918919
11 HGD 0.637931 0.837209
12 GCG 0.6 0.860465
13 KGT 0.592593 0.923077
14 TGG 0.587302 0.9
15 TS5 0.573529 0.880952
16 GSB 0.528571 0.878049
17 0HH 0.528571 0.782609
18 GSO 0.521127 0.857143
19 BOB 0.493506 0.75
20 GTB 0.493333 0.631579
21 GBI 0.486842 0.782609
22 48T 0.481013 0.8
23 ESG 0.480519 0.62069
24 GTD 0.480519 0.6
25 L9X 0.480519 0.62069
26 1R4 0.474359 0.62069
27 GIP 0.474359 0.6
28 GPS 0.468354 0.72
29 GPR 0.468354 0.72
30 GBP 0.468354 0.6
31 GAZ 0.457831 0.679245
32 GVX 0.45679 0.8
33 HFV 0.447761 0.8
34 ASV 0.446154 0.9
35 GNB 0.445783 0.6
36 VB1 0.444444 0.9
37 W05 0.444444 0.923077
38 LZ6 0.436782 0.692308
39 ACV 0.430769 0.878049
40 BCV 0.424242 0.9
41 CDH 0.424242 0.818182
42 2G2 0.42029 0.615385
43 HGA 0.42 0.622222
44 MEQ 0.411765 0.658537
45 M8F 0.411765 0.837209
46 TS4 0.410256 0.804348
47 M9F 0.405797 0.837209
48 M2W 0.4 0.8
49 KKA 0.4 0.894737
50 ACW 0.4 0.8
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5VE5; Ligand: GSH; Similar sites found: 16
This union binding pocket(no: 1) in the query (biounit: 5ve5.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1F06 NDP 0.03657 0.40281 1.875
2 1F06 2NP 0.03657 0.40281 1.875
3 4HVA 4HV 0.01273 0.41926 2.26415
4 2H6T IVA VAL VAL STA ALA STA 0.04501 0.40283 4.41176
5 3RE4 TO1 0.008993 0.41015 4.65116
6 1IDA 0PO 0.02725 0.41048 5.05051
7 1BAI 0Q4 0.02069 0.4086 5.64516
8 3FV3 IVA VAL VAL STA ALA STA 0.0276 0.40098 7.66962
9 1SIV PSI 0.01677 0.41811 12.1212
10 3S43 478 0.01506 0.41687 12.1212
11 4NJS G08 0.0298 0.40417 12.1212
12 4Q5M ROC 0.03584 0.40005 12.8079
13 2P3B 3TL 0.04045 0.40346 23.2323
14 1QH5 GSH 0.00002797 0.5449 32.3077
15 1QH5 GBP 0.00003779 0.53543 32.3077
16 4YSL GSH 0.00000006874 0.64612 40.8163
Pocket No.: 2; Query (leader) PDB : 5VE5; Ligand: GSH; Similar sites found: 2
This union binding pocket(no: 2) in the query (biounit: 5ve5.bio3) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2VBF TPP 0.0281 0.40691 5.57029
2 4RL0 3S0 0.01136 0.4004 13.5279
Pocket No.: 3; Query (leader) PDB : 5VE5; Ligand: GSH; Similar sites found: 38
This union binding pocket(no: 3) in the query (biounit: 5ve5.bio2) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5A3T MMK 0.03381 0.40677 1.06101
2 5W0N 2KH 0.01338 0.4052 1.06101
3 5U3B 7TD 0.03027 0.40622 1.67224
4 4E5N NAD 0.0384 0.4084 2.12121
5 3ZYR ASN NAG NAG BMA MAN MAN NAG NAG 0.03328 0.4033 2.29885
6 3ZYR NAG NAG BMA MAN MAN NAG NAG 0.0344 0.4024 2.29885
7 5GUE GGS 0.01321 0.41496 2.41692
8 3EWC MCF 0.03048 0.40537 2.42588
9 5TO8 7FM 0.03156 0.40968 2.83688
10 4S3R 7SA 0.04021 0.40061 2.91777
11 2C49 ADN 0.009662 0.41737 2.98013
12 1Q9I FAD 0.04525 0.41839 3.18302
13 1Q9I TEO 0.04525 0.41839 3.18302
14 4Q0L V14 0.02558 0.40426 3.42205
15 5VAH SAH 0.01698 0.40452 3.49345
16 5VBC SAH 0.02129 0.40104 3.49345
17 4M52 M52 0.02725 0.40286 3.97878
18 5CSS G3P 0.01712 0.40194 3.9823
19 1QSR ACO 0.03517 0.4013 4.24403
20 4OAV ACP 0.01197 0.40452 4.50928
21 5TWO 7MV 0.01585 0.40552 5.14706
22 5TDF 7A3 0.01188 0.41222 5.30504
23 2Q8Z NUP 0.02616 0.40577 5.55556
24 3P3G 3P3 0.01933 0.41532 5.66667
25 3P3G UKW 0.01933 0.41532 5.66667
26 2Q2V NAD 0.02211 0.41641 7.05882
27 1PS9 NAP 0.01361 0.42627 7.1618
28 5I0U DCY 0.01866 0.40039 7.5
29 2IS6 ADP 0.01383 0.40965 7.69231
30 4G17 0VN 0.01331 0.40546 7.87879
31 3SSO SAH 0.02632 0.41868 8.48806
32 5G3N X28 0.02176 0.40526 9.44882
33 3FSM 2NC 0.01724 0.42584 9.85222
34 3BJK CIT 0.02609 0.40837 11.1111
35 4NMC FAD 0.04436 0.40801 12.7321
36 4NMC 2OP 0.04278 0.40801 12.7321
37 3NWQ 2NC 0.02362 0.41097 20.202
38 5T2Z 017 0.03462 0.40669 23.2323
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