scPDB - 4cgg entry

Protein Data Bank Entry:

PDB ID : 4cgg

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2013-11-25

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	62 %
B	38 %

Ligand binding site composition:

B-Factor:	22.817
Number of residues:	29
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.944	405.000

% Hydrophobic	% Polar
47.50	52.50
According to VolSite

Ligand :

HET Code:	K5Q
Formula:	C22H17NO7
Molecular weight:	407.373 g/mol
DrugBank ID:	-
Buried Surface Area:	55.31 %
Polar Surface area:	131.31 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	1
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
32.2076	-7.9032	11.646

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
C6	CB	GLN- 95	4.13	0	Hydrophobic	false
C6	CB	ALA- 98	4.28	0	Hydrophobic	false
C21	CG	TYR- 99	3.81	0	Hydrophobic	false
C11	CB	TYR- 99	4.09	0	Hydrophobic	false
C1	CD2	LEU- 102	3.72	0	Hydrophobic	false
C4	CG2	THR- 125	3.9	0	Hydrophobic	false
C1	CB	ALA- 129	3.79	0	Hydrophobic	false
C5	CB	TRP- 132	3.76	0	Hydrophobic	false
O26	N	GLU- 170	3.08	149.64	H-Bond (Protein Donor)	false
C19	CB	HIS- 171	4.43	0	Hydrophobic	false
O24	N	HIS- 171	2.99	159.39	H-Bond (Protein Donor)	false
O24	ND1	HIS- 171	3.45	128.29	H-Bond (Protein Donor)	false
O28	ND1	HIS- 171	2.86	157.31	H-Bond (Protein Donor)	false
C19	CG	LYS- 173	4.49	0	Hydrophobic	false
O25	NZ	LYS- 173	3.42	161.33	H-Bond (Protein Donor)	false
O25	NZ	LYS- 173	3.42	0	Ionic (Protein Cationic)	false
O27	NZ	LYS- 173	2.92	0	Ionic (Protein Cationic)	false
C8	CG2	THR- 174	4.4	0	Hydrophobic	false
C3	CG2	THR- 174	3.76	0	Hydrophobic	false
C9	CB	THR- 174	4.23	0	Hydrophobic	false
O24	OG1	THR- 174	2.64	162.74	H-Bond (Protein Donor)	false
C5	CE	MET- 178	3.49	0	Hydrophobic	false
C5	CE	MET- 178	3.49	0	Hydrophobic	false