scPDB - 3vri entry

Protein Data Bank Entry:

PDB ID : 3vri

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2012-04-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	HLA class I histocompatibility antigen, B-57 alpha chain
ID:	1B57_HUMAN
AC:	P18465
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	83 %
C	17 %

Ligand binding site composition:

B-Factor:	12.924
Number of residues:	32
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.212	313.875

% Hydrophobic	% Polar
65.59	34.41
According to VolSite

Ligand :

HET Code:	1KX
Formula:	C14H18N6O
Molecular weight:	286.332 g/mol
DrugBank ID:	DB01048
Buried Surface Area:	72.08 %
Polar Surface area:	101.88 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
14.1929	-10.5727	43.0033

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
C07	CB	ALA- 3	4.21	0	Hydrophobic	false
C08	CE1	TYR- 9	3.59	0	Hydrophobic	false
C	CG2	ILE- 10	3.74	0	Hydrophobic	false
O	OH	TYR- 74	2.76	161.91	H-Bond (Protein Donor)	false
C	CD1	ILE- 95	4.02	0	Hydrophobic	false
C13	CG2	ILE- 95	4.18	0	Hydrophobic	false
C09	CG1	VAL- 97	3.94	0	Hydrophobic	false
C12	CG2	VAL- 97	4.42	0	Hydrophobic	false
C09	CD1	TYR- 99	4.04	0	Hydrophobic	false
C08	CE1	TYR- 99	3.5	0	Hydrophobic	false
N01	OD1	ASP- 114	2.88	149.72	H-Bond (Ligand Donor)	false
N01	OD2	ASP- 114	3.28	139.31	H-Bond (Ligand Donor)	false
N05	OD2	ASP- 114	3.1	147.7	H-Bond (Ligand Donor)	false
N04	OG	SER- 116	2.78	146.15	H-Bond (Protein Donor)	false
N05	OG	SER- 116	3.15	128.21	H-Bond (Ligand Donor)	false
C13	CB	SER- 116	3.36	0	Hydrophobic	false
C13	CD2	TYR- 123	3.54	0	Hydrophobic	false
N05	O	ILE- 124	3.08	143.23	H-Bond (Ligand Donor)	false
C04	CD2	LEU- 156	4.44	0	Hydrophobic	false
C07	CD1	LEU- 156	4.46	0	Hydrophobic	false