scPDB - 1w5y entry

Protein Data Bank Entry:

PDB ID : 1w5y

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2004-08-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Gag-Pol polyprotein
ID:	POL_HV1B1
AC:	P03366
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11678
EC Number:	3.4.23.16

Chains:

Chain Name:	Percentage of Residues within binding site
A	47 %
B	53 %

Ligand binding site composition:

B-Factor:	15.504
Number of residues:	45
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.987	921.375

% Hydrophobic	% Polar
43.22	56.78
According to VolSite

Ligand :

HET Code:	BE6
Formula:	C38H36F4N2O8
Molecular weight:	724.695 g/mol
DrugBank ID:	-
Buried Surface Area:	72.32 %
Polar Surface area:	157.57 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	6
Rings:	6
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
13.2553	23.1566	5.63429

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
F49	CD	ARG- 8	3.75	0	Hydrophobic	false
F50	CD	ARG- 8	3.45	0	Hydrophobic	false
C01	CD2	LEU- 23	4.35	0	Hydrophobic	false
C02	CD2	LEU- 23	3.41	0	Hydrophobic	false
C12	CD2	LEU- 23	3.54	0	Hydrophobic	false
O24	OD1	ASP- 25	2.78	129.6	H-Bond (Ligand Donor)	false
O24	OD2	ASP- 25	2.79	157.79	H-Bond (Ligand Donor)	false
O25	OD2	ASP- 25	2.73	156.15	H-Bond (Ligand Donor)	false
N21	O	GLY- 27	3	163.13	H-Bond (Ligand Donor)	false
N28	O	GLY- 27	3.25	166.42	H-Bond (Ligand Donor)	false
O36	O	GLY- 27	3.36	154.18	H-Bond (Ligand Donor)	false
O46	O	GLY- 27	3.19	137.2	H-Bond (Ligand Donor)	false
C33	CB	ALA- 28	3.54	0	Hydrophobic	false
C43	CB	ALA- 28	3.45	0	Hydrophobic	false
O36	N	ASP- 29	3.15	158.99	H-Bond (Protein Donor)	false
O46	N	ASP- 29	2.98	151.95	H-Bond (Protein Donor)	false
C48	CB	ASP- 29	4.42	0	Hydrophobic	false
C37	CB	ASP- 30	3.88	0	Hydrophobic	false
C47	CB	ASP- 30	3.86	0	Hydrophobic	false
C33	CG1	VAL- 32	3.81	0	Hydrophobic	false
C44	CG2	VAL- 32	3.5	0	Hydrophobic	false
C37	CG2	ILE- 47	4.26	0	Hydrophobic	false
C41	CB	ILE- 47	4.34	0	Hydrophobic	false
C47	CG2	ILE- 47	3.87	0	Hydrophobic	false
C34	CD1	ILE- 47	3.99	0	Hydrophobic	false
C44	CD1	ILE- 47	4.01	0	Hydrophobic	false
C15	CD1	ILE- 50	4.28	0	Hydrophobic	false
C42	CD1	ILE- 50	4.29	0	Hydrophobic	false
F51	CB	ILE- 50	4.34	0	Hydrophobic	false
F52	CG1	ILE- 50	4.09	0	Hydrophobic	false
C13	CD1	ILE- 50	3.62	0	Hydrophobic	false
C33	CD1	ILE- 50	3.59	0	Hydrophobic	false
C09	CB	PRO- 81	4.07	0	Hydrophobic	false
F51	CG	PRO- 81	3.4	0	Hydrophobic	false
F52	CG	PRO- 81	3.98	0	Hydrophobic	false
C06	CG	PRO- 81	4.14	0	Hydrophobic	false
F51	CG1	VAL- 82	4.19	0	Hydrophobic	false
C01	CG1	VAL- 82	3.61	0	Hydrophobic	false
C07	CG2	VAL- 82	3.72	0	Hydrophobic	false
C07	CG2	VAL- 82	3.72	0	Hydrophobic	false
C11	CG2	VAL- 82	3.72	0	Hydrophobic	false
C01	CG1	VAL- 82	3.61	0	Hydrophobic	false
C33	CD1	ILE- 84	4.38	0	Hydrophobic	false
C43	CD1	ILE- 84	4.38	0	Hydrophobic	false
C23	CD1	ILE- 84	3.45	0	Hydrophobic	false
C13	CD1	ILE- 84	3.42	0	Hydrophobic	false