scPDB - 1bvg entry

Protein Data Bank Entry:

PDB ID : 1bvg

Resolution : Å

Experimental Method : NMR

Deposition Date : 1996-01-16

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:	3.4.23.16

Chains:

Chain Name:	Percentage of Residues within binding site
A	52 %
B	48 %

Ligand binding site composition:

B-Factor:	0.570
Number of residues:	45
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.321	769.500

% Hydrophobic	% Polar
54.39	45.61
According to VolSite

Ligand :

HET Code:	DMP
Formula:	C35H38N2O5
Molecular weight:	566.687 g/mol
DrugBank ID:	-
Buried Surface Area:	65.72 %
Polar Surface area:	104.47 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
1.2241	-4.67024	-5.15074

Binding mode :

What is Poseview ?

2D View
3D View

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
C36	CD2	LEU- 23	4.19	0	Hydrophobic	false
C66	CD2	LEU- 23	4.11	0	Hydrophobic	false
O4	OD1	ASP- 25	2.68	155.67	H-Bond (Ligand Donor)	false
O4	OD1	ASP- 25	2.74	126.48	H-Bond (Ligand Donor)	false
O5	OD1	ASP- 25	2.99	175.69	H-Bond (Ligand Donor)	false
C26	CB	ALA- 28	3.77	0	Hydrophobic	false
C76	CB	ALA- 28	3.68	0	Hydrophobic	false
C24	CB	ALA- 28	3.48	0	Hydrophobic	false
C74	CB	ALA- 28	3.36	0	Hydrophobic	false
O27	N	ASP- 29	3.43	139.3	H-Bond (Protein Donor)	false
O77	N	ASP- 29	2.93	140.82	H-Bond (Protein Donor)	false
C27	CB	ASP- 30	4.28	0	Hydrophobic	false
C77	CB	ASP- 30	4.33	0	Hydrophobic	false
O27	N	ASP- 30	3.32	134.62	H-Bond (Protein Donor)	false
O77	N	ASP- 30	3.04	144.53	H-Bond (Protein Donor)	false
C27	CB	VAL- 32	4.34	0	Hydrophobic	false
C27	CG2	ILE- 47	4.42	0	Hydrophobic	false
C21	CD1	ILE- 47	3.89	0	Hydrophobic	false
C23	CD1	ILE- 47	3.49	0	Hydrophobic	false
C73	CD1	ILE- 47	3.62	0	Hydrophobic	false
C30	CD1	ILE- 50	3.86	0	Hydrophobic	false
C33	CG1	ILE- 50	4	0	Hydrophobic	false
C60	CD1	ILE- 50	3.89	0	Hydrophobic	false
C63	CG1	ILE- 50	4.02	0	Hydrophobic	false
C21	CG1	ILE- 50	4.11	0	Hydrophobic	false
C25	CD1	ILE- 50	3.61	0	Hydrophobic	false
C32	CG1	ILE- 50	3.84	0	Hydrophobic	false
C62	CG1	ILE- 50	3.88	0	Hydrophobic	false
C71	CG1	ILE- 50	4.13	0	Hydrophobic	false
C75	CD1	ILE- 50	3.61	0	Hydrophobic	false
O1	N	ILE- 50	3.23	153.4	H-Bond (Protein Donor)	false
O1	N	ILE- 50	3.25	154.73	H-Bond (Protein Donor)	false
C33	CG	PRO- 81	3.76	0	Hydrophobic	false
C63	CG	PRO- 81	3.76	0	Hydrophobic	false
C33	CB	VAL- 82	4.08	0	Hydrophobic	false
C34	CG2	VAL- 82	4	0	Hydrophobic	false
C63	CB	VAL- 82	4.22	0	Hydrophobic	false
C64	CG2	VAL- 82	4.23	0	Hydrophobic	false
C25	CG2	ILE- 84	3.83	0	Hydrophobic	false
C30	CD1	ILE- 84	3.44	0	Hydrophobic	false
C60	CD1	ILE- 84	3.41	0	Hydrophobic	false
C75	CG2	ILE- 84	4	0	Hydrophobic	false