scPDB - 4cjk entry

Protein Data Bank Entry:

PDB ID : 4cjk

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2013-12-21

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	54 %
B	46 %

Ligand binding site composition:

B-Factor:	21.363
Number of residues:	25
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.465	320.625

% Hydrophobic	% Polar
53.68	46.32
According to VolSite

Ligand :

HET Code:	H39
Formula:	C21H25N2O5
Molecular weight:	385.434 g/mol
DrugBank ID:	-
Buried Surface Area:	50.14 %
Polar Surface area:	103.48 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
10.8265	-45.9675	13.3961

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
C13	CG	GLN- 95	3.87	0	Hydrophobic	false
C9	CG	GLN- 95	3.52	0	Hydrophobic	false
C2	CB	ALA- 98	4.16	0	Hydrophobic	false
C13	CD1	TYR- 99	4.4	0	Hydrophobic	false
C2	CB	TYR- 99	3.96	0	Hydrophobic	false
C1	CD1	LEU- 102	4.43	0	Hydrophobic	false
C14	CD1	LEU- 102	4.35	0	Hydrophobic	false
C21	CG2	THR- 125	4.36	0	Hydrophobic	false
C1	CG2	THR- 125	4.02	0	Hydrophobic	false
C14	CB	ALA- 128	4.08	0	Hydrophobic	false
C18	CB	ALA- 128	4.43	0	Hydrophobic	false
C14	CB	ALA- 129	4.33	0	Hydrophobic	false
C14	CB	TRP- 132	4.23	0	Hydrophobic	false
O25	N	GLU- 170	2.93	162.73	H-Bond (Protein Donor)	false
O24	N	HIS- 171	2.96	160.04	H-Bond (Protein Donor)	false
C10	CB	THR- 174	4.25	0	Hydrophobic	false
C17	CG2	THR- 174	3.84	0	Hydrophobic	false
C7	CG2	THR- 174	3.66	0	Hydrophobic	false
O24	OG1	THR- 174	2.61	159.09	H-Bond (Protein Donor)	false
C20	CE	MET- 178	3.7	0	Hydrophobic	false