scPDB - 1hvr entry

Protein Data Bank Entry:

PDB ID : 1hvr

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 1994-02-14

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:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	49 %
B	51 %

Ligand binding site composition:

B-Factor:	24.629
Number of residues:	43
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.030	749.250

% Hydrophobic	% Polar
44.59	55.41
According to VolSite

Ligand :

HET Code:	XK2
Formula:	C41H38N2O3
Molecular weight:	606.752 g/mol
DrugBank ID:	-
Buried Surface Area:	70.63 %
Polar Surface area:	64.01 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	2
Rings:	7
Aromatic rings:	6
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-9.19157	15.9063	27.9465

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
C37	CD2	LEU- 23	4.29	0	Hydrophobic	false
C63	CD2	LEU- 23	4.28	0	Hydrophobic	false
O4	OD1	ASP- 25	2.91	158.72	H-Bond (Ligand Donor)	false
O4	OD1	ASP- 25	3.33	122.69	H-Bond (Ligand Donor)	false
O5	OD2	ASP- 25	3.03	137.26	H-Bond (Ligand Donor)	false
O5	OD1	ASP- 25	3.13	163.6	H-Bond (Ligand Donor)	false
C5	CB	ALA- 28	4.45	0	Hydrophobic	false
C22	CB	ALA- 28	3.52	0	Hydrophobic	false
C78	CB	ALA- 28	3.58	0	Hydrophobic	false
C74	CB	ASP- 29	4.26	0	Hydrophobic	false
C25	CB	ASP- 30	3.46	0	Hydrophobic	false
C75	CB	ASP- 30	3.48	0	Hydrophobic	false
C76	CG1	VAL- 32	4.5	0	Hydrophobic	false
C78	CG1	VAL- 32	3.8	0	Hydrophobic	false
C24	CG2	VAL- 32	3.4	0	Hydrophobic	false
C27	CB	ILE- 47	4.17	0	Hydrophobic	false
C74	CG2	ILE- 47	4.48	0	Hydrophobic	false
C26	CG2	ILE- 47	3.78	0	Hydrophobic	false
C72	CD1	ILE- 47	4.1	0	Hydrophobic	false
C76	CD1	ILE- 47	3.88	0	Hydrophobic	false
C77	CD1	ILE- 47	3.78	0	Hydrophobic	false
C23	CD1	ILE- 47	4.07	0	Hydrophobic	false
O1	N	ILE- 50	3.24	134.84	H-Bond (Protein Donor)	false
O1	N	ILE- 50	3.17	160.6	H-Bond (Protein Donor)	false
C21	CD1	ILE- 50	4.29	0	Hydrophobic	false
C33	CG1	ILE- 50	4.06	0	Hydrophobic	false
C67	CD1	ILE- 50	3.63	0	Hydrophobic	false
C79	CD1	ILE- 50	3.63	0	Hydrophobic	false
C25	CD2	LEU- 76	4.06	0	Hydrophobic	false
C34	CG	PRO- 81	3.95	0	Hydrophobic	false
C66	CG	PRO- 81	3.52	0	Hydrophobic	false
C65	CG2	VAL- 82	4.37	0	Hydrophobic	false
C36	CG1	VAL- 82	3.95	0	Hydrophobic	false
C61	CD1	ILE- 84	4.22	0	Hydrophobic	false
C67	CD1	ILE- 84	4.36	0	Hydrophobic	false
C21	CD1	ILE- 84	4.03	0	Hydrophobic	false
C31	CD1	ILE- 84	3.62	0	Hydrophobic	false
C79	CD1	ILE- 84	3.96	0	Hydrophobic	false