scPDB - 3pxv entry

Protein Data Bank Entry:

PDB ID : 3pxv

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2010-12-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Nitroreductase
ID:	B8FRE0_DESHD
AC:	B8FRE0
Organism:	Desulfitobacterium hafniense
Reign:	Bacteria
TaxID:	272564
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	65 %
B	35 %

Ligand binding site composition:

B-Factor:	46.797
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.903	921.375

% Hydrophobic	% Polar
46.15	53.85
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	71.28 %
Polar Surface area:	217.05 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
35.2262	62.2639	92.1613

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
O2P	NH1	ARG- 12	2.87	160.81	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 12	3.17	166.71	H-Bond (Protein Donor)	false
O2P	CZ	ARG- 12	3.64	0	Ionic (Protein Cationic)	false
C1'	CB	SER- 14	4.39	0	Hydrophobic	false
C3'	CB	SER- 14	4.34	0	Hydrophobic	false
O1P	N	SER- 14	3.1	146.37	H-Bond (Protein Donor)	false
O2P	OG	SER- 14	2.58	150.72	H-Bond (Protein Donor)	false
N1	NH2	ARG- 16	3.2	133.3	H-Bond (Protein Donor)	false
O2	NE	ARG- 16	2.95	152.48	H-Bond (Protein Donor)	false
O2	NH2	ARG- 16	3.36	132.68	H-Bond (Protein Donor)	false
O2'	NH2	ARG- 16	3.08	130.88	H-Bond (Protein Donor)	false
C8M	CB	PRO- 39	4.09	0	Hydrophobic	false
C4'	CB	ASN- 43	3.74	0	Hydrophobic	false
O2	OH	TYR- 90	2.54	139.19	H-Bond (Protein Donor)	false
C7M	CG1	VAL- 110	3.46	0	Hydrophobic	false
C7M	CD1	ILE- 114	3.88	0	Hydrophobic	false
C8M	CD1	ILE- 114	3.32	0	Hydrophobic	false
C1'	CG1	ILE- 131	4.4	0	Hydrophobic	false
C7M	CG	MET- 132	4.25	0	Hydrophobic	false
C8M	CE	MET- 132	3.68	0	Hydrophobic	false
C8	CB	MET- 132	3.56	0	Hydrophobic	false
N5	N	GLY- 134	3.1	164.44	H-Bond (Protein Donor)	false
O4	N	TYR- 135	2.83	155.77	H-Bond (Protein Donor)	false
C6	SG	CYS- 163	4.42	0	Hydrophobic	false
C7M	SG	CYS- 163	4.04	0	Hydrophobic	false
O1P	NZ	LYS- 174	3.19	0	Ionic (Protein Cationic)	false
C5'	CB	HIS- 177	3.91	0	Hydrophobic	false
O3P	N	HIS- 177	2.76	175.45	H-Bond (Protein Donor)	false