scPDB - 2vpy entry

Protein Data Bank Entry:

PDB ID : 2vpy

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2008-03-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thiosulfate reductase
ID:	Q72LA4_THET2
AC:	Q72LA4
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	262724
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	40.889
Number of residues:	58
Including
Standard Amino Acids:	52
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.358	772.875

% Hydrophobic	% Polar
41.92	58.08
According to VolSite

Ligand :

HET Code:	MGD
Formula:	C20H24N10O13P2S2
Molecular weight:	738.541 g/mol
DrugBank ID:	-
Buried Surface Area:	77.29 %
Polar Surface area:	440.93 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	10
Rings:	6
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
118.67	145.485	19.6972

Binding mode :

What is Poseview ?

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C10	CE1	PHE- 48	4.17	0	Hydrophobic	false
O1A	ND1	HIS- 145	2.92	141.56	H-Bond (Protein Donor)	false
C10	CG	PRO- 168	4.23	0	Hydrophobic	false
C11	CB	PRO- 168	3.96	0	Hydrophobic	false
C23	CB	PRO- 168	4.35	0	Hydrophobic	false
C23	CB	LEU- 172	3.98	0	Hydrophobic	false
O1B	ND2	ASN- 441	3.28	143.45	H-Bond (Protein Donor)	false
O2A	N	ASN- 441	2.91	171.6	H-Bond (Protein Donor)	false
O3B	OG	SER- 445	3.47	125.71	H-Bond (Protein Donor)	false
O3A	OG	SER- 445	2.96	165.3	H-Bond (Protein Donor)	false
O2A	OG	SER- 445	2.92	124.75	H-Bond (Protein Donor)	false
N22	O	SER- 445	3.25	158.84	H-Bond (Ligand Donor)	false
C23	CB	SER- 445	4.11	0	Hydrophobic	false
N2	O	ILE- 465	2.96	165.13	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 466	2.68	146.95	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 466	2.56	174.65	H-Bond (Ligand Donor)	false
O2'	NE2	GLN- 470	3.31	129.54	H-Bond (Protein Donor)	false
N1	OE1	GLU- 482	2.54	147.68	H-Bond (Ligand Donor)	false
N2	OE1	GLU- 482	2.83	129.39	H-Bond (Ligand Donor)	false
O17	NH1	ARG- 625	2.86	147.8	H-Bond (Protein Donor)	false
C10	CE1	PHE- 631	3.73	0	Hydrophobic	false
C11	CE2	PHE- 631	4.27	0	Hydrophobic	false
O1B	N	ALA- 632	3.02	123.68	H-Bond (Protein Donor)	false
O2B	NH1	ARG- 633	2.96	168.03	H-Bond (Protein Donor)	false
O2B	CZ	ARG- 633	3.67	0	Ionic (Protein Cationic)	false
C5'	CD	ARG- 633	4.02	0	Hydrophobic	false
C2'	CB	ARG- 633	3.7	0	Hydrophobic	false
N18	OD2	ASP- 716	3.16	150.57	H-Bond (Ligand Donor)	false
N19	OD2	ASP- 716	3.28	142.85	H-Bond (Ligand Donor)	false
N19	OD1	ASN- 717	3.17	154.77	H-Bond (Ligand Donor)	false
N19	OE1	GLN- 720	2.98	131.28	H-Bond (Ligand Donor)	false
O6	O	HOH- 2386	2.74	179.95	H-Bond (Protein Donor)	false