scPDB - 2nya entry

Protein Data Bank Entry:

PDB ID : 2nya

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2006-11-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Periplasmic nitrate reductase
ID:	NAPA_ECOLI
AC:	P33937
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	1.7.99.4

Chains:

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

Ligand binding site composition:

B-Factor:	22.708
Number of residues:	65
Including
Standard Amino Acids:	59
Non Standard Amino Acids:	2
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.558	243.000

% Hydrophobic	% Polar
51.39	48.61
According to VolSite

Ligand :

HET Code:	MGD
Formula:	C20H24N10O13P2S2
Molecular weight:	738.541 g/mol
DrugBank ID:	-
Buried Surface Area:	83.26 %
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
9.08511	-2.10028	42.1275

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
C23	CB	CYS- 13	4.18	0	Hydrophobic	false
N2	O	TRP- 176	2.75	161.31	H-Bond (Ligand Donor)	false
O1A	N	ASN- 179	3.02	139.92	H-Bond (Protein Donor)	false
N19	O	GLU- 182	3.42	144.77	H-Bond (Ligand Donor)	false
N22	O	MET- 183	2.92	136.98	H-Bond (Ligand Donor)	false
C23	CB	MET- 183	3.97	0	Hydrophobic	false
C11	CB	MET- 183	4.29	0	Hydrophobic	false
O2'	OG	SER- 207	2.83	149.49	H-Bond (Ligand Donor)	false
C2'	CB	THR- 208	4.24	0	Hydrophobic	false
O2'	N	THR- 208	3.25	163.11	H-Bond (Protein Donor)	false
C5'	CZ	TYR- 209	4.03	0	Hydrophobic	false
C3'	CE2	TYR- 209	3.48	0	Hydrophobic	false
O6	N	GLN- 226	3.3	167.84	H-Bond (Protein Donor)	false
N1	OD2	ASP- 228	2.72	146.99	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 228	2.81	140.32	H-Bond (Ligand Donor)	false
C10	CG2	THR- 335	3.56	0	Hydrophobic	false
O2A	N	MET- 336	3.01	159.92	H-Bond (Protein Donor)	false
C10	CG	MET- 336	3.82	0	Hydrophobic	false
O1B	NE	ARG- 684	3.14	163.35	H-Bond (Protein Donor)	false
O2B	N	ARG- 684	2.95	164.88	H-Bond (Protein Donor)	false
C10	CD	ARG- 684	3.69	0	Hydrophobic	false
C14	CD	ARG- 684	4.2	0	Hydrophobic	false
N19	O	VAL- 685	3.03	135.75	H-Bond (Ligand Donor)	false
N18	O	HIS- 688	2.67	162.14	H-Bond (Ligand Donor)	false
C14	CZ3	TRP- 689	3.6	0	Hydrophobic	false
N15	NE2	HIS- 690	3.45	150.53	H-Bond (Ligand Donor)	false
O17	N	HIS- 690	2.82	153.46	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 783	2.99	171.72	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 783	2.99	0	Ionic (Protein Cationic)	false
O2A	O	HOH- 4123	2.95	166.12	H-Bond (Protein Donor)	false