scPDB - 3ekw entry

Protein Data Bank Entry:

PDB ID : 3ekw

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2008-09-19

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_HV1A2
AC:	P03369
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11685
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:	19.809
Number of residues:	44
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.082	799.875

% Hydrophobic	% Polar
45.99	54.01
According to VolSite

Ligand :

HET Code:	DR7
Formula:	C38H52N6O7
Molecular weight:	704.855 g/mol
DrugBank ID:	DB01072
Buried Surface Area:	67.48 %
Polar Surface area:	171.21 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	5
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
19.8268	0.0412745	18.1455

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
DuAr	CZ	ARG- 8	3.95	156.77	Pi/Cation	false
CAT	CD2	LEU- 23	4.09	0	Hydrophobic	false
CAZ	CD1	LEU- 23	3.66	0	Hydrophobic	false
OAM	OD2	ASP- 25	2.61	168.69	H-Bond (Ligand Donor)	false
OAM	OD1	ASP- 25	2.62	151.08	H-Bond (Protein Donor)	false
NBG	O	GLY- 27	3.21	161.73	H-Bond (Ligand Donor)	false
NBH	O	GLY- 27	3.06	164.17	H-Bond (Ligand Donor)	false
CAE	CB	ALA- 28	3.94	0	Hydrophobic	false
CAF	CB	ALA- 28	3.84	0	Hydrophobic	false
CAA	CB	ASP- 29	4.49	0	Hydrophobic	false
OAI	N	ASP- 29	2.92	165.88	H-Bond (Protein Donor)	false
OAJ	N	ASP- 29	3.02	167.59	H-Bond (Protein Donor)	false
CG1	CB	ASP- 30	4.36	0	Hydrophobic	false
CAH	CB	ASP- 30	4.22	0	Hydrophobic	false
CAE	CG2	VAL- 32	4.12	0	Hydrophobic	false
CG1	CG2	VAL- 32	4.08	0	Hydrophobic	false
CAH	CG2	VAL- 32	4.49	0	Hydrophobic	false
CG2	CD1	ILE- 47	3.83	0	Hydrophobic	false
CG1	CD1	ILE- 47	4.48	0	Hydrophobic	false
CAG	CD1	ILE- 47	3.86	0	Hydrophobic	false
CAA	CG1	VAL- 48	4.26	0	Hydrophobic	false
N	O	VAL- 48	2.89	169.13	H-Bond (Ligand Donor)	false
NBF	O	VAL- 48	3.14	163.53	H-Bond (Ligand Donor)	false
CAF	CD1	ILE- 50	4.17	0	Hydrophobic	false
CAG	CG1	ILE- 50	3.82	0	Hydrophobic	false
CAE	CD1	ILE- 50	3.62	0	Hydrophobic	false
CAV	CB	PRO- 81	4.33	0	Hydrophobic	false
CAN	CB	PRO- 81	3.9	0	Hydrophobic	false
CAY	CG	PRO- 81	3.31	0	Hydrophobic	false
CAP	CB	ALA- 82	3.92	0	Hydrophobic	false
CAE	CD1	ILE- 84	3.76	0	Hydrophobic	false
CAF	CD1	ILE- 84	3.97	0	Hydrophobic	false
CAU	CD1	ILE- 84	3.8	0	Hydrophobic	false
CBB	CD1	ILE- 84	4.17	0	Hydrophobic	false
OBJ	O	HOH- 513	3.23	130.08	H-Bond (Protein Donor)	false