scPDB - 4ced entry

Protein Data Bank Entry:

PDB ID : 4ced

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2013-11-11

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	61 %
B	39 %

Ligand binding site composition:

B-Factor:	15.992
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.646	381.375

% Hydrophobic	% Polar
47.79	52.21
According to VolSite

Ligand :

HET Code:	9NS
Formula:	C29H29N2O8
Molecular weight:	533.549 g/mol
DrugBank ID:	-
Buried Surface Area:	51.82 %
Polar Surface area:	145.4 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:	13

Mass center Coordinates

X	Y	Z
33.6187	-7.72169	13.65

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
C7	CG	GLN- 95	4.1	0	Hydrophobic	false
C28	CG	GLU- 96	4.48	0	Hydrophobic	false
C7	CB	ALA- 98	4.43	0	Hydrophobic	false
C22	CD1	TYR- 99	4.3	0	Hydrophobic	false
C23	CB	TYR- 99	4.24	0	Hydrophobic	false
C28	CB	TYR- 99	3.78	0	Hydrophobic	false
C29	CG	TYR- 99	3.9	0	Hydrophobic	false
C14	CB	TYR- 99	4.2	0	Hydrophobic	false
C6	CG2	THR- 125	4.25	0	Hydrophobic	false
N30	O	GLN- 168	2.74	168.39	H-Bond (Ligand Donor)	false
O35	N	GLU- 170	2.84	161.88	H-Bond (Protein Donor)	false
C22	CB	HIS- 171	4.16	0	Hydrophobic	false
O32	N	HIS- 171	2.92	165.12	H-Bond (Protein Donor)	false
C22	CG	LYS- 173	3.93	0	Hydrophobic	false
C29	CD	LYS- 173	4.25	0	Hydrophobic	false
C15	CB	THR- 174	4.22	0	Hydrophobic	false
C11	CG2	THR- 174	4.07	0	Hydrophobic	false
O32	OG1	THR- 174	2.74	163.66	H-Bond (Protein Donor)	false