scPDB - 4i7f entry

Protein Data Bank Entry:

PDB ID : 4i7f

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2012-11-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Gag-Pol polyprotein
ID:	POL_HV1H2
AC:	P04585
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11706
EC Number:	2.7.7.49

Chains:

Chain Name:	Percentage of Residues within binding site
A	92 %
B	8 %

Ligand binding site composition:

B-Factor:	58.076
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.170	904.500

% Hydrophobic	% Polar
57.46	42.54
According to VolSite

Ligand :

HET Code:	NVE
Formula:	C27H33N4O5P
Molecular weight:	524.548 g/mol
DrugBank ID:	-
Buried Surface Area:	71.78 %
Polar Surface area:	103.9 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	0
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
8.6053	10.0189	16.0426

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
C17	CG	PRO- 95	3.46	0	Hydrophobic	false
C16	CD1	LEU- 100	4.28	0	Hydrophobic	false
C17	CD2	LEU- 100	4.06	0	Hydrophobic	false
C10	CD1	LEU- 100	3.7	0	Hydrophobic	false
C28	CB	LYS- 103	4.36	0	Hydrophobic	false
C35	CB	SER- 105	3.42	0	Hydrophobic	false
C20	CB	SER- 105	4.4	0	Hydrophobic	false
C1	CG2	VAL- 106	3.73	0	Hydrophobic	false
C11	CG2	VAL- 106	4.06	0	Hydrophobic	false
C27	CG2	VAL- 106	3.71	0	Hydrophobic	false
C26	CB	VAL- 106	3.63	0	Hydrophobic	false
O25	N	VAL- 106	2.92	152.69	H-Bond (Protein Donor)	false
O34	N	VAL- 106	3.33	129.54	H-Bond (Protein Donor)	false
C36	CG2	THR- 107	3.36	0	Hydrophobic	false
C1	CG1	VAL- 179	3.99	0	Hydrophobic	false
C2	CB	TYR- 181	4.09	0	Hydrophobic	false
C17	CB	TYR- 181	4.28	0	Hydrophobic	false
C17	CD2	TYR- 181	3.32	0	Hydrophobic	false
C2	CB	TYR- 188	3.92	0	Hydrophobic	false
C20	CD1	ILE- 195	4.12	0	Hydrophobic	false
C35	CD1	ILE- 195	4.3	0	Hydrophobic	false
C24	CG	PRO- 225	3.41	0	Hydrophobic	false
C24	CG	PRO- 236	4.47	0	Hydrophobic	false
C31	CG	PRO- 236	4.41	0	Hydrophobic	false
C26	CB	PRO- 236	4.38	0	Hydrophobic	false
C32	CZ	TYR- 318	3.4	0	Hydrophobic	false