scPDB - 2npx entry

Protein Data Bank Entry:

PDB ID : 2npx

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 1992-05-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NADH peroxidase
ID:	NAPE_ENTFA
AC:	P37062
Organism:	Enterococcus faecalis
Reign:	Bacteria
TaxID:	226185
EC Number:	1.11.1.1

Chains:

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

Ligand binding site composition:

B-Factor:	14.623
Number of residues:	59
Including
Standard Amino Acids:	53
Non Standard Amino Acids:	2
Water Molecules:	4
Cofactors:	NAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.656	924.750

% Hydrophobic	% Polar
32.48	67.52
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	70.3 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
35.7818	40.5704	120.752

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
O2A	OG	SER- 9	2.62	161.04	H-Bond (Protein Donor)	false
C4B	CB	SER- 9	3.88	0	Hydrophobic	false
C4'	CB	HIS- 10	4.41	0	Hydrophobic	false
O4'	ND1	HIS- 10	3.2	175.11	H-Bond (Protein Donor)	false
O1P	N	GLY- 11	3.1	159.35	H-Bond (Protein Donor)	false
O3B	OE1	GLU- 32	2.56	132.98	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 32	2.76	169.23	H-Bond (Ligand Donor)	false
N3A	N	LYS- 33	3.27	156.58	H-Bond (Protein Donor)	false
C8	CB	SER- 41	4.09	0	Hydrophobic	false
O2'	OD1	OCS- 42	3.37	122.54	H-Bond (Ligand Donor)	false
O2'	OD2	OCS- 42	2.79	161.52	H-Bond (Ligand Donor)	false
N6A	O	ILE- 79	2.8	167.23	H-Bond (Ligand Donor)	false
N1A	N	ILE- 79	2.94	170.55	H-Bond (Protein Donor)	false
O1P	OG	SER- 110	3.02	148.43	H-Bond (Protein Donor)	false
O1A	N	ALA- 113	3.28	152.91	H-Bond (Protein Donor)	false
C7M	CE	MET- 131	4.2	0	Hydrophobic	false
C8M	CG	ARG- 132	4.1	0	Hydrophobic	false
C7M	CG1	ILE- 160	3.82	0	Hydrophobic	false
C8M	CD1	ILE- 160	3.52	0	Hydrophobic	false
O3'	OD1	ASP- 281	2.79	161.2	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 281	3.4	139.8	H-Bond (Ligand Donor)	false
C5'	CB	ASP- 281	4.18	0	Hydrophobic	false
O2P	N	ASP- 281	2.81	165.25	H-Bond (Protein Donor)	false
N1	N	ALA- 299	3.23	157.8	H-Bond (Protein Donor)	false
O2	N	ALA- 299	2.96	139.17	H-Bond (Protein Donor)	false
C2'	CB	ALA- 299	4.11	0	Hydrophobic	false
C5'	CB	ALA- 302	4.44	0	Hydrophobic	false
O1P	O	HOH- 866	2.71	179.98	H-Bond (Protein Donor)	false
O2P	O	HOH- 897	2.83	179.95	H-Bond (Protein Donor)	false