scPDB - 4cf8 entry

Protein Data Bank Entry:

PDB ID : 4cf8

Resolution :1.650 Å

Experimental Method : X-ray

Deposition Date : 2013-11-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Integrase
ID:	Q76353_9HIV1
AC:	Q76353
Organism:	Human immunodeficiency virus 1
Reign:	Viruses
TaxID:	11676
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	38 %
B	62 %

Ligand binding site composition:

B-Factor:	16.795
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.898	415.125

% Hydrophobic	% Polar
53.66	46.34
According to VolSite

Ligand :

HET Code:	V7H
Formula:	C28H27N2O7
Molecular weight:	503.523 g/mol
DrugBank ID:	-
Buried Surface Area:	53.62 %
Polar Surface area:	144.43 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	2
Rings:	4
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
9.71051	32.8052	-0.0927027

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
C12	CG	GLN- 95	3.9	0	Hydrophobic	false
C15	CG	GLN- 95	4.27	0	Hydrophobic	false
C4	CG	GLN- 95	3.71	0	Hydrophobic	false
C15	CG	GLU- 96	4.48	0	Hydrophobic	false
C36	CB	ALA- 98	4.44	0	Hydrophobic	false
C3	CB	ALA- 98	4.49	0	Hydrophobic	false
C11	CD1	TYR- 99	4.3	0	Hydrophobic	false
C12	CB	TYR- 99	4.25	0	Hydrophobic	false
C15	CB	TYR- 99	3.8	0	Hydrophobic	false
C14	CG	TYR- 99	3.88	0	Hydrophobic	false
C4	CB	TYR- 99	4.16	0	Hydrophobic	false
C36	CG2	THR- 125	4.39	0	Hydrophobic	false
C2	CG2	THR- 125	4.38	0	Hydrophobic	false
C37	CB	ALA- 128	3.57	0	Hydrophobic	false
C35	CB	ALA- 129	3.59	0	Hydrophobic	false
C33	CB	TRP- 132	3.95	0	Hydrophobic	false
N30	O	GLN- 168	2.98	165.81	H-Bond (Ligand Donor)	false
O8	N	GLU- 170	2.96	162.66	H-Bond (Protein Donor)	false
C11	CB	HIS- 171	4.32	0	Hydrophobic	false
O9	N	HIS- 171	2.96	162.31	H-Bond (Protein Donor)	false
C11	CD	LYS- 173	4.02	0	Hydrophobic	false
C14	CD	LYS- 173	4.37	0	Hydrophobic	false
C5	CB	THR- 174	4.17	0	Hydrophobic	false
C6	CG2	THR- 174	3.89	0	Hydrophobic	false
O9	OG1	THR- 174	2.68	164.54	H-Bond (Protein Donor)	false
C33	CE	MET- 178	3.39	0	Hydrophobic	false