scPDB - 2zcv entry

Protein Data Bank Entry:

PDB ID : 2zcv

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2007-11-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Quinone oxidoreductase 2
ID:	QOR2_ECOLI
AC:	P39315
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	1.6.5.2

Chains:

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

Ligand binding site composition:

B-Factor:	37.691
Number of residues:	42
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.801	523.125

% Hydrophobic	% Polar
42.58	57.42
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	54.39 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
24.3661	10.3784	8.53006

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
O3B	OG1	THR- 8	3.48	163.97	H-Bond (Ligand Donor)	false
O3X	OG1	THR- 8	2.93	144	H-Bond (Protein Donor)	false
O2A	N	GLN- 10	3.08	167.78	H-Bond (Protein Donor)	false
O2N	N	LEU- 11	2.66	167.87	H-Bond (Protein Donor)	false
C5D	CB	LEU- 11	3.81	0	Hydrophobic	false
O2B	NE	ARG- 33	3.47	130.54	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 33	3.24	135.88	H-Bond (Protein Donor)	false
O1X	NH2	ARG- 33	2.66	155.24	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 33	3.51	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 33	3.96	149.88	Pi/Cation	false
C5D	CG2	ILE- 72	3.91	0	Hydrophobic	false
O1A	OG	SER- 75	3.4	125.02	H-Bond (Protein Donor)	false
C5B	CB	SER- 75	3.71	0	Hydrophobic	false
C2D	CB	SER- 75	4.09	0	Hydrophobic	false
N7N	O	GLY- 138	2.8	138.99	H-Bond (Ligand Donor)	false
O5D	OH	TYR- 140	3.45	172.06	H-Bond (Protein Donor)	false
O7N	N	TYR- 140	3.14	139.32	H-Bond (Protein Donor)	false
C4N	CD1	TYR- 140	3.35	0	Hydrophobic	false
O7N	ND2	ASN- 143	3.37	139.85	H-Bond (Protein Donor)	false
O1N	NE	ARG- 171	2.95	164.27	H-Bond (Protein Donor)	false
O1N	NH2	ARG- 171	3.45	134.87	H-Bond (Protein Donor)	false
O1N	CZ	ARG- 171	3.64	0	Ionic (Protein Cationic)	false
O2N	O	HOH- 1011	2.91	129.21	H-Bond (Protein Donor)	false
N7N	O	HOH- 1059	3.34	123.52	H-Bond (Ligand Donor)	false