scPDB - 3s85 entry

Protein Data Bank Entry:

PDB ID : 3s85

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2011-05-27

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_HV1N5
AC:	P12497
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
G	4 %
J	2 %
K	46 %
L	48 %

Ligand binding site composition:

B-Factor:	47.638
Number of residues:	46
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.209	1515.375

% Hydrophobic	% Polar
48.33	51.67
According to VolSite

Ligand :

HET Code:	LK0
Formula:	C39H53N5O7
Molecular weight:	703.867 g/mol
DrugBank ID:	-
Buried Surface Area:	64.14 %
Polar Surface area:	167.97 Å2

Number of
H-Bond Acceptors:	8
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
27.6541	1.81761	69.3468

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
C8	CD2	LEU- 23	4.3	0	Hydrophobic	false
C10	CD2	LEU- 23	4.14	0	Hydrophobic	false
C16	CD2	LEU- 23	4.31	0	Hydrophobic	false
O51	OD2	ASP- 25	2.67	161.86	H-Bond (Ligand Donor)	false
O51	OD1	ASP- 25	3.2	121.51	H-Bond (Ligand Donor)	false
N1	O	GLY- 27	3	144.53	H-Bond (Ligand Donor)	false
N6	O	GLY- 27	3.13	134.63	H-Bond (Ligand Donor)	false
C30	CB	ALA- 28	3.77	0	Hydrophobic	false
C39	CB	ALA- 28	3.9	0	Hydrophobic	false
O31	N	ASP- 29	3.06	158.76	H-Bond (Protein Donor)	false
O41	OD2	ASP- 29	2.88	147.78	H-Bond (Protein Donor)	false
O41	N	ASP- 29	3.04	165.23	H-Bond (Protein Donor)	false
C42	CB	ASP- 29	4.44	0	Hydrophobic	false
C39	CB	ASP- 30	4.4	0	Hydrophobic	false
C40	CG1	VAL- 32	4.11	0	Hydrophobic	false
C30	CG2	VAL- 32	3.87	0	Hydrophobic	false
C48	CG	GLU- 35	4.48	0	Hydrophobic	false
C29	CD1	ILE- 47	4.36	0	Hydrophobic	false
C50	CD1	ILE- 47	3.61	0	Hydrophobic	false
C39	CD1	ILE- 47	4.45	0	Hydrophobic	false
C43	CD1	ILE- 47	3.78	0	Hydrophobic	false
N34	O	GLY- 48	3.31	145.18	H-Bond (Ligand Donor)	false
C30	CD1	ILE- 50	3.87	0	Hydrophobic	false
C50	CD1	ILE- 50	3.9	0	Hydrophobic	false
C40	CD1	ILE- 50	4.16	0	Hydrophobic	false
C43	CG2	ILE- 50	3.84	0	Hydrophobic	false
C19	CG	PRO- 81	3.9	0	Hydrophobic	false
C44	CB	PRO- 81	3.67	0	Hydrophobic	false
C49	CB	PRO- 81	4.03	0	Hydrophobic	false
C13	CG	PRO- 81	3.45	0	Hydrophobic	false
C11	CG1	VAL- 82	3.67	0	Hydrophobic	false
C17	CG2	VAL- 82	4.22	0	Hydrophobic	false
C30	CD1	ILE- 84	4.22	0	Hydrophobic	false
C40	CD1	ILE- 84	3.96	0	Hydrophobic	false
C8	CD1	ILE- 84	3.87	0	Hydrophobic	false
C5	CD1	ILE- 84	4.07	0	Hydrophobic	false