scPDB - 1hvj entry

Protein Data Bank Entry:

PDB ID : 1hvj

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 1994-01-26

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_HV1B5
AC:	P04587
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11682
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	50 %
B	50 %

Ligand binding site composition:

B-Factor:	13.235
Number of residues:	42
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.322	1012.500

% Hydrophobic	% Polar
44.00	56.00
According to VolSite

Ligand :

HET Code:	A78
Formula:	C44H58N8O5
Molecular weight:	778.982 g/mol
DrugBank ID:	-
Buried Surface Area:	58.88 %
Polar Surface area:	168.88 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:	2
Rotatable Bonds:	19

Mass center Coordinates

X	Y	Z
5.32595	-1.46781	14.1989

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
DuAr	CZ	ARG- 8	3.52	170.45	Pi/Cation	false
DuAr	CZ	ARG- 8	3.59	168.8	Pi/Cation	false
C15	CD	ARG- 8	3.47	0	Hydrophobic	false
C40	CD2	LEU- 23	4.38	0	Hydrophobic	false
C15	CD2	LEU- 23	4.14	0	Hydrophobic	false
O48	OD2	ASP- 25	2.99	137.52	H-Bond (Ligand Donor)	false
O48	OD1	ASP- 25	2.69	154.62	H-Bond (Ligand Donor)	false
N38	O	GLY- 27	3.12	160.07	H-Bond (Ligand Donor)	false
C27	CB	ALA- 28	4.12	0	Hydrophobic	false
C86	CB	ALA- 28	4.23	0	Hydrophobic	false
C87	CB	ALA- 28	4.46	0	Hydrophobic	false
O2	N	ASP- 29	2.99	171.74	H-Bond (Protein Donor)	false
O98	N	ASP- 29	2.89	165.12	H-Bond (Protein Donor)	false
C28	CG2	VAL- 32	4.12	0	Hydrophobic	false
C87	CG2	VAL- 32	3.98	0	Hydrophobic	false
C28	CD1	ILE- 47	4.26	0	Hydrophobic	false
C87	CD1	ILE- 47	4.06	0	Hydrophobic	false
N22	O	GLY- 48	2.96	166.91	H-Bond (Ligand Donor)	false
N81	O	GLY- 48	3.19	160.6	H-Bond (Ligand Donor)	false
C45	CD1	ILE- 50	3.93	0	Hydrophobic	false
C46	CG1	ILE- 50	3.79	0	Hydrophobic	false
C27	CG1	ILE- 50	3.62	0	Hydrophobic	false
C58	CG1	ILE- 50	3.96	0	Hydrophobic	false
C86	CG1	ILE- 50	3.88	0	Hydrophobic	false
C56	CB	PRO- 81	3.89	0	Hydrophobic	false
C57	CG	PRO- 81	3.89	0	Hydrophobic	false
C44	CG	PRO- 81	4.12	0	Hydrophobic	false
C15	CG1	VAL- 82	4.29	0	Hydrophobic	false
C55	CG1	VAL- 82	3.74	0	Hydrophobic	false
C41	CG1	VAL- 82	4.1	0	Hydrophobic	false
C27	CG2	ILE- 84	4.37	0	Hydrophobic	false
C86	CD1	ILE- 84	3.56	0	Hydrophobic	false
C46	CD1	ILE- 84	3.98	0	Hydrophobic	false
C52	CD1	ILE- 84	3.94	0	Hydrophobic	false