scPDB - 4xrq entry

Protein Data Bank Entry:

PDB ID : 4xrq

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2015-01-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Gag polyprotein
ID:	GAG_HV1N5
AC:	P12493
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11698
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	26.090
Number of residues:	20
Including
Standard Amino Acids:	19
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.487	236.250

% Hydrophobic	% Polar
55.71	44.29
According to VolSite

Ligand :

HET Code:	1B0
Formula:	C27H27N3O2
Molecular weight:	425.522 g/mol
DrugBank ID:	-
Buried Surface Area:	47.04 %
Polar Surface area:	65.2 Å2

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

Mass center Coordinates

X	Y	Z
30.2274	-1.82456	-0.180094

Binding mode :

What is Poseview ?

2D View
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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
C6	CB	ASN- 53	4.2	0	Hydrophobic	false
C8	CB	LEU- 56	3.55	0	Hydrophobic	false
C12	CD1	LEU- 56	3.9	0	Hydrophobic	false
C9	CB	LEU- 56	3.71	0	Hydrophobic	false
N4	OD1	ASN- 57	2.63	175.97	H-Bond (Ligand Donor)	false
O14	ND2	ASN- 57	2.95	175.74	H-Bond (Protein Donor)	false
N3	OE1	GLN- 63	3.03	142.94	H-Bond (Ligand Donor)	false
C10	CB	MET- 66	3.77	0	Hydrophobic	false
C11	CG	LEU- 69	3.98	0	Hydrophobic	false
C10	CD2	LEU- 69	4.04	0	Hydrophobic	false
O24	NZ	LYS- 70	3.11	162.32	H-Bond (Protein Donor)	false
C7	CD	LYS- 70	4.36	0	Hydrophobic	false
C19	CG	LYS- 70	4.06	0	Hydrophobic	false
C11	CG	LYS- 70	3.42	0	Hydrophobic	false
C10	CD	LYS- 70	4.07	0	Hydrophobic	false
DuAr	NZ	LYS- 70	3.47	22.2	Pi/Cation	false
C21	CG2	ILE- 73	3.92	0	Hydrophobic	false
C11	CD1	ILE- 73	3.98	0	Hydrophobic	false
C21	CB	ALA- 105	4.1	0	Hydrophobic	false
C22	CG2	THR- 107	3.39	0	Hydrophobic	false