scPDB - 2vpz entry

Protein Data Bank Entry:

PDB ID : 2vpz

Resolution :2.400 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:	35.518
Number of residues:	58
Including
Standard Amino Acids:	55
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.207	685.125

% Hydrophobic	% Polar
47.29	52.71
According to VolSite

Ligand :

HET Code:	MGD
Formula:	C20H24N10O13P2S2
Molecular weight:	738.541 g/mol
DrugBank ID:	-
Buried Surface Area:	82.88 %
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
112.632	145.513	32.854

Binding mode :

What is Poseview ?

2D View
3D View

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
O3A	NE2	HIS- 209	3.15	135.55	H-Bond (Protein Donor)	false
O2A	N	HIS- 209	3.32	143.02	H-Bond (Protein Donor)	false
C4'	CB	HIS- 209	4.27	0	Hydrophobic	false
N22	OD1	ASP- 213	2.93	131.68	H-Bond (Ligand Donor)	false
C23	CB	ASP- 213	4.22	0	Hydrophobic	false
N20	N	THR- 214	3.09	171.6	H-Bond (Protein Donor)	false
N2	O	VAL- 235	3	145.18	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 236	2.66	154.06	H-Bond (Ligand Donor)	false
O3'	NE	ARG- 238	3.2	134.46	H-Bond (Protein Donor)	false
O3'	NH2	ARG- 238	2.68	161.42	H-Bond (Protein Donor)	false
O6	N	GLY- 255	3.06	167.18	H-Bond (Protein Donor)	false
N1	OD2	ASP- 257	2.85	152.04	H-Bond (Ligand Donor)	false
N1	OD1	ASP- 257	3.37	132.72	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 257	2.85	153.57	H-Bond (Ligand Donor)	false
O2B	OG1	THR- 331	2.56	156.89	H-Bond (Protein Donor)	false
O1A	N	ARG- 332	3.31	133.69	H-Bond (Protein Donor)	false
C11	CD	ARG- 332	4.48	0	Hydrophobic	false
O1A	N	HIS- 333	2.99	168.14	H-Bond (Protein Donor)	false
C10	CB	HIS- 333	4.01	0	Hydrophobic	false
O1B	NE1	TRP- 336	3.48	131.62	H-Bond (Protein Donor)	false
N7	OH	TYR- 337	3.44	136.52	H-Bond (Protein Donor)	false
O6	OH	TYR- 337	2.94	141.09	H-Bond (Protein Donor)	false
C10	CG	ARG- 625	4.15	0	Hydrophobic	false
N19	O	SER- 626	3.04	129.12	H-Bond (Ligand Donor)	false
N18	O	HIS- 629	2.92	173.61	H-Bond (Ligand Donor)	false
C14	CZ	PHE- 631	4.25	0	Hydrophobic	false
O17	N	PHE- 631	2.81	170.83	H-Bond (Protein Donor)	false
C3'	CE1	TYR- 694	4.35	0	Hydrophobic	false
O1B	NH2	ARG- 735	2.88	149.04	H-Bond (Protein Donor)	false
O1B	NH1	ARG- 735	3.22	134.22	H-Bond (Protein Donor)	false
O4'	NH1	ARG- 735	3.39	121.93	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 735	3.48	0	Ionic (Protein Cationic)	false