scPDB - 3zcm entry

Protein Data Bank Entry:

PDB ID : 3zcm

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2012-11-21

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	58 %
B	42 %

Ligand binding site composition:

B-Factor:	15.204
Number of residues:	26
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.950	340.875

% Hydrophobic	% Polar
50.50	49.50
According to VolSite

Ligand :

HET Code:	PX3
Formula:	C28H28N2O6
Molecular weight:	488.532 g/mol
DrugBank ID:	-
Buried Surface Area:	52.6 %
Polar Surface area:	101.36 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	4
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-34.355	32.4591	-14.4733

Binding mode :

What is Poseview ?

2D View
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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
C5	CG	GLN- 95	4.31	0	Hydrophobic	false
C8	CB	GLN- 95	4.01	0	Hydrophobic	false
C8	CB	ALA- 98	4.43	0	Hydrophobic	false
C25	CB	ALA- 98	4.03	0	Hydrophobic	false
C16	CB	TYR- 99	4.32	0	Hydrophobic	false
C23	CD1	TYR- 99	3.87	0	Hydrophobic	false
C25	CD2	LEU- 102	3.85	0	Hydrophobic	false
C10	CG2	THR- 125	4.05	0	Hydrophobic	false
C5	CG2	THR- 125	4	0	Hydrophobic	false
C7	CB	ALA- 128	3.65	0	Hydrophobic	false
C25	CB	ALA- 129	3.88	0	Hydrophobic	false
C18	CB	ALA- 129	4.18	0	Hydrophobic	false
N32	O	GLN- 168	2.84	157.33	H-Bond (Ligand Donor)	false
O36	N	GLU- 170	2.84	167.62	H-Bond (Protein Donor)	false
C4	CB	GLU- 170	4.13	0	Hydrophobic	false
O34	N	HIS- 171	2.93	164.87	H-Bond (Protein Donor)	false
C9	CG2	THR- 174	3.91	0	Hydrophobic	false
C12	CG2	THR- 174	4.15	0	Hydrophobic	false
C17	CB	THR- 174	4.22	0	Hydrophobic	false
C25	CG2	THR- 174	4.35	0	Hydrophobic	false
O34	OG1	THR- 174	2.83	162.63	H-Bond (Protein Donor)	false
C6	CE	MET- 178	3.68	0	Hydrophobic	false