scPDB - 4cif entry

Protein Data Bank Entry:

PDB ID : 4cif

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2013-12-07

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	44 %
B	56 %

Ligand binding site composition:

B-Factor:	20.071
Number of residues:	25
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.022	384.750

% Hydrophobic	% Polar
52.63	47.37
According to VolSite

Ligand :

HET Code:	JDX
Formula:	C26H28N2O5
Molecular weight:	448.511 g/mol
DrugBank ID:	-
Buried Surface Area:	51.81 %
Polar Surface area:	92.13 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
10.7509	-45.8722	1.02052

Binding mode :

What is Poseview ?

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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
C23	CG	GLN- 95	4.38	0	Hydrophobic	false
C24	CB	GLN- 95	4.06	0	Hydrophobic	false
C24	CB	ALA- 98	4.23	0	Hydrophobic	false
C12	CB	ALA- 98	4.27	0	Hydrophobic	false
C25	CB	TYR- 99	4.24	0	Hydrophobic	false
C27	CD1	TYR- 99	4.37	0	Hydrophobic	false
C12	CD2	LEU- 102	3.78	0	Hydrophobic	false
C9	CG2	THR- 125	4.03	0	Hydrophobic	false
C23	CG2	THR- 125	3.93	0	Hydrophobic	false
C10	CB	ALA- 128	3.67	0	Hydrophobic	false
C12	CB	ALA- 129	3.88	0	Hydrophobic	false
C8	CB	ALA- 129	4.13	0	Hydrophobic	false
N3	O	GLN- 168	2.76	163.9	H-Bond (Ligand Donor)	false
O33	N	GLU- 170	2.85	159.31	H-Bond (Protein Donor)	false
C17	CB	GLU- 170	4.2	0	Hydrophobic	false
O32	N	HIS- 171	2.97	162.97	H-Bond (Protein Donor)	false
C7	CG2	THR- 174	4.39	0	Hydrophobic	false
C12	CG2	THR- 174	4.21	0	Hydrophobic	false
C30	CG2	THR- 174	4.22	0	Hydrophobic	false
O32	OG1	THR- 174	2.76	167.41	H-Bond (Protein Donor)	false
C6	CE	MET- 178	3.55	0	Hydrophobic	false