scPDB - 4nvk entry

Protein Data Bank Entry:

PDB ID : 4nvk

Resolution :1.560 Å

Experimental Method : X-ray

Deposition Date : 2013-12-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Peroxidase
ID:	B3LRE1_YEAS1
AC:	B3LRE1
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	285006
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	19.285
Number of residues:	24
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.323	1069.875

% Hydrophobic	% Polar
48.26	51.74
According to VolSite

Ligand :

HET Code:	2NY
Formula:	C12H16N4
Molecular weight:	216.282 g/mol
DrugBank ID:	-
Buried Surface Area:	83.42 %
Polar Surface area:	55.04 Å2

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

Mass center Coordinates

X	Y	Z
19.634	2.60812	-2.48869

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
CAG	CB	HIS- 175	3.8	0	Hydrophobic	false
CAE	CG2	THR- 180	3.59	0	Hydrophobic	false
CAB	CB	ALA- 192	4.32	0	Hydrophobic	false
CAA	CB	PHE- 200	4.39	0	Hydrophobic	false
CAH	CD2	TYR- 227	4.19	0	Hydrophobic	false
CAB	CE2	TYR- 227	4.03	0	Hydrophobic	false
C5	SD	MET- 228	4.28	0	Hydrophobic	false
CAA	CE	MET- 229	4.4	0	Hydrophobic	false
CAE	CD1	LEU- 230	4.14	0	Hydrophobic	false
NAC	OD2	ASP- 233	2.9	149.13	H-Bond (Ligand Donor)	false
N1	O	HOH- 495	3.3	120.77	H-Bond (Protein Donor)	false