scPDB - 1bv9 entry

Protein Data Bank Entry:

PDB ID : 1bv9

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 1998-09-22

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	51 %
B	49 %

Ligand binding site composition:

B-Factor:	20.099
Number of residues:	51
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.808	658.125

% Hydrophobic	% Polar
44.62	55.38
According to VolSite

Ligand :

HET Code:	XV6
Formula:	C41H38N6O5S2
Molecular weight:	758.908 g/mol
DrugBank ID:	DB02702
Buried Surface Area:	65.49 %
Polar Surface area:	204.47 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	4
Rings:	7
Aromatic rings:	6
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
-9.16413	15.9127	27.8321

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
C37	CD2	LEU- 23	4.38	0	Hydrophobic	false
O4	OD1	ASP- 25	2.72	155.01	H-Bond (Ligand Donor)	false
O4	OD2	ASP- 25	3.21	134.94	H-Bond (Ligand Donor)	false
O5	OD1	ASP- 25	3.11	157.12	H-Bond (Ligand Donor)	false
O5	OD2	ASP- 25	3.14	145.87	H-Bond (Ligand Donor)	false
C5	CB	ALA- 28	4.47	0	Hydrophobic	false
C24	CB	ALA- 28	3.47	0	Hydrophobic	false
C74	CB	ALA- 28	3.5	0	Hydrophobic	false
S29	CB	ASP- 29	4.21	0	Hydrophobic	false
S79	CB	ASP- 29	4.37	0	Hydrophobic	false
O76	N	ASP- 29	3.45	122.97	H-Bond (Protein Donor)	false
O26	N	ASP- 30	3.1	143.52	H-Bond (Protein Donor)	false
O76	N	ASP- 30	3.23	133.1	H-Bond (Protein Donor)	false
C24	CG1	VAL- 32	3.8	0	Hydrophobic	false
C74	CG1	VAL- 32	3.62	0	Hydrophobic	false
S29	CG2	ILE- 47	4.42	0	Hydrophobic	false
S79	CG2	ILE- 47	3.8	0	Hydrophobic	false
C22	CD1	ILE- 47	3.91	0	Hydrophobic	false
C72	CD1	ILE- 47	4.16	0	Hydrophobic	false
N26	O	GLY- 48	3.02	168.87	H-Bond (Ligand Donor)	false
N76	O	GLY- 48	3.14	157.29	H-Bond (Ligand Donor)	false
N27	N	GLY- 48	2.93	173.9	H-Bond (Protein Donor)	false
N77	N	GLY- 48	3.22	171.04	H-Bond (Protein Donor)	false
O1	N	ILE- 50	3.1	169.14	H-Bond (Protein Donor)	false
O1	N	ILE- 50	3.15	170.46	H-Bond (Protein Donor)	false
C33	CD1	ILE- 50	3.76	0	Hydrophobic	false
C34	CG1	ILE- 50	4.29	0	Hydrophobic	false
C67	CG1	ILE- 50	3.76	0	Hydrophobic	false
C25	CD1	ILE- 50	3.52	0	Hydrophobic	false
C75	CD1	ILE- 50	3.56	0	Hydrophobic	false
C34	CG	PRO- 81	3.94	0	Hydrophobic	false
C66	CG	PRO- 81	3.45	0	Hydrophobic	false
C34	CG2	VAL- 82	3.73	0	Hydrophobic	false
C65	CG1	VAL- 82	3.4	0	Hydrophobic	false
C31	CG2	VAL- 84	4.43	0	Hydrophobic	false
C24	CG1	VAL- 84	3.59	0	Hydrophobic	false
C74	CG1	VAL- 84	3.74	0	Hydrophobic	false