scPDB - 9hvp entry

Protein Data Bank Entry:

PDB ID : 9hvp

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 1990-11-06

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_HV1N5
AC:	P12497
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11698
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	56 %
B	44 %

Ligand binding site composition:

B-Factor:	10.400
Number of residues:	41
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.992	695.250

% Hydrophobic	% Polar
47.57	52.43
According to VolSite

Ligand :

HET Code:	0E9
Formula:	C43H52N4O7
Molecular weight:	736.896 g/mol
DrugBank ID:	-
Buried Surface Area:	59.31 %
Polar Surface area:	155.08 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	5
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	20

Mass center Coordinates

X	Y	Z
-8.87231	15.7609	28.2052

Binding mode :

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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
C6A	CD1	LEU- 23	4	0	Hydrophobic	false
C2B	CD1	LEU- 23	3.46	0	Hydrophobic	false
O3	OD1	ASP- 25	3.22	156.09	H-Bond (Ligand Donor)	false
O3	OD1	ASP- 25	2.87	124.11	H-Bond (Ligand Donor)	false
N2	O	GLY- 27	3.43	141.04	H-Bond (Ligand Donor)	false
CG1	CB	ALA- 28	3.92	0	Hydrophobic	false
CG11	CB	ALA- 28	3.5	0	Hydrophobic	false
O1	N	ASP- 29	3.05	157.42	H-Bond (Protein Donor)	false
O11	N	ASP- 29	2.8	150.35	H-Bond (Protein Donor)	false
C22	CB	ASP- 29	4.45	0	Hydrophobic	false
CG1	CG1	VAL- 32	4.01	0	Hydrophobic	false
CG2	CG1	VAL- 32	3.94	0	Hydrophobic	false
CG11	CG1	VAL- 32	4.05	0	Hydrophobic	false
CG2	CD1	ILE- 47	3.78	0	Hydrophobic	false
CG21	CD1	ILE- 47	3.53	0	Hydrophobic	false
C8	CG2	ILE- 47	3.35	0	Hydrophobic	false
N	O	GLY- 48	2.73	152.19	H-Bond (Ligand Donor)	false
N1	O	GLY- 48	3.09	144.74	H-Bond (Ligand Donor)	false
CG11	CG2	ILE- 50	4.2	0	Hydrophobic	false
CB	CG1	ILE- 50	4.02	0	Hydrophobic	false
C2A	CG2	ILE- 50	4.17	0	Hydrophobic	false
C6B	CG2	ILE- 50	3.99	0	Hydrophobic	false
CB1	CG1	ILE- 50	3.84	0	Hydrophobic	false
C5B	CG	PRO- 81	4.26	0	Hydrophobic	false
C4A	CG	PRO- 81	3.62	0	Hydrophobic	false
C5A	CG2	VAL- 82	4.13	0	Hydrophobic	false
C5B	CG2	VAL- 82	3.76	0	Hydrophobic	false
CG1	CD1	ILE- 84	3.52	0	Hydrophobic	false
CG11	CD1	ILE- 84	3.67	0	Hydrophobic	false
C6B	CD1	ILE- 84	4.02	0	Hydrophobic	false
C2A	CD1	ILE- 84	3.5	0	Hydrophobic	false