scPDB - 3ekp entry

Protein Data Bank Entry:

PDB ID : 3ekp

Resolution :2.150 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	49 %
B	51 %

Ligand binding site composition:

B-Factor:	35.608
Number of residues:	43
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.075	951.750

% Hydrophobic	% Polar
44.33	55.67
According to VolSite

Ligand :

HET Code:	478
Formula:	C25H35N3O6S
Molecular weight:	505.627 g/mol
DrugBank ID:	DB00701
Buried Surface Area:	68.41 %
Polar Surface area:	139.57 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
11.7733	-21.2676	35.794

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
C24	CD2	LEU- 23	3.86	0	Hydrophobic	false
C9	CD2	LEU- 23	3.92	0	Hydrophobic	false
O3	OD1	ASP- 25	2.64	147.42	H-Bond (Protein Donor)	false
O3	OD1	ASP- 25	2.53	131.17	H-Bond (Ligand Donor)	false
O3	OD2	ASP- 25	2.89	152.61	H-Bond (Ligand Donor)	false
N1	O	GLY- 27	3.33	168.27	H-Bond (Ligand Donor)	false
C14	CB	ALA- 28	4.07	0	Hydrophobic	false
C2	CB	ALA- 28	3.5	0	Hydrophobic	false
C19	CB	ALA- 28	3.35	0	Hydrophobic	false
C20	CB	ASP- 30	4.48	0	Hydrophobic	false
N3	O	ASP- 30	3.35	131.24	H-Bond (Ligand Donor)	false
N3	OD2	ASP- 30	3.36	126.13	H-Bond (Ligand Donor)	false
C25	CG2	VAL- 32	3.28	0	Hydrophobic	false
C19	CG2	VAL- 32	3.38	0	Hydrophobic	false
C1	CB	ILE- 47	4.14	0	Hydrophobic	false
C4	CD1	ILE- 47	4.32	0	Hydrophobic	false
C21	CB	ILE- 47	4.43	0	Hydrophobic	false
C25	CD1	ILE- 47	4.44	0	Hydrophobic	false
C20	CD1	ILE- 47	4.39	0	Hydrophobic	false
C10	CB	ILE- 50	4.35	0	Hydrophobic	false
C23	CG1	ILE- 50	3.93	0	Hydrophobic	false
C2	CD1	ILE- 50	3.61	0	Hydrophobic	false
C18	CD1	ILE- 50	3.88	0	Hydrophobic	false
C13	CG	PRO- 81	3.51	0	Hydrophobic	false
C11	CB	ALA- 82	3.78	0	Hydrophobic	false
C18	CD1	ILE- 84	4.49	0	Hydrophobic	false
C24	CG2	ILE- 84	4.41	0	Hydrophobic	false
C2	CD1	ILE- 84	3.5	0	Hydrophobic	false
C8	CD1	ILE- 84	3.78	0	Hydrophobic	false
O1	O	HOH- 612	3.23	179.99	H-Bond (Protein Donor)	false