scPDB - 3bxr entry

Protein Data Bank Entry:

PDB ID : 3bxr

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2008-01-14

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_HV1A2
AC:	P03369
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11685
EC Number:	3.4.23.16

Chains:

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

Ligand binding site composition:

B-Factor:	9.789
Number of residues:	41
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.878	796.500

% Hydrophobic	% Polar
42.37	57.63
According to VolSite

Ligand :

HET Code:	DRR
Formula:	C37H51N5O7
Molecular weight:	677.830 g/mol
DrugBank ID:	-
Buried Surface Area:	65.03 %
Polar Surface area:	163.95 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	5
Rings:	6
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
5.36804	-1.49267	13.7393

Binding mode :

What is Poseview ?

2D View
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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
CBD	CD2	LEU- 23	3.68	0	Hydrophobic	false
NAM	O	GLY- 27	2.88	153.95	H-Bond (Ligand Donor)	false
CG2	CB	ALA- 28	3.64	0	Hydrophobic	false
OAE	N	ASP- 29	2.87	165.72	H-Bond (Protein Donor)	false
CG1	CB	ASP- 30	4.33	0	Hydrophobic	false
CG1	CG2	VAL- 32	4	0	Hydrophobic	false
CG2	CG2	VAL- 32	4.42	0	Hydrophobic	false
CB	CG1	ILE- 47	4.5	0	Hydrophobic	false
CG1	CD1	ILE- 47	3.59	0	Hydrophobic	false
N	O	GLY- 48	2.87	172.67	H-Bond (Ligand Donor)	false
CBQ	CD1	ILE- 50	3.53	0	Hydrophobic	false
CAQ	CD1	ILE- 50	3.62	0	Hydrophobic	false
CBF	CG	PRO- 81	4.2	0	Hydrophobic	false
CBG	CB	PRO- 81	3.64	0	Hydrophobic	false
CBE	CG1	VAL- 82	3.63	0	Hydrophobic	false
CG2	CD1	ILE- 84	3.78	0	Hydrophobic	false
CBB	CD1	ILE- 84	3.59	0	Hydrophobic	false
CAR	CD2	LEU- 123	3.62	0	Hydrophobic	false
OAY	ND2	ASN- 125	2.68	154.36	H-Bond (Protein Donor)	false
NBM	O	GLY- 127	3.04	165.77	H-Bond (Ligand Donor)	false
CBO	CB	ALA- 128	3.83	0	Hydrophobic	false
OBT	N	ASP- 129	2.87	166.42	H-Bond (Protein Donor)	false
CBR	CG2	VAL- 132	3.56	0	Hydrophobic	false
CBP	CD1	ILE- 147	4.11	0	Hydrophobic	false
NBU	O	GLY- 148	3.04	165.81	H-Bond (Ligand Donor)	false
CG2	CD1	ILE- 150	3.94	0	Hydrophobic	false
CAW	CG	PRO- 181	4.07	0	Hydrophobic	false
CAS	CG	PRO- 181	3.68	0	Hydrophobic	false
CAU	CG2	VAL- 182	3.71	0	Hydrophobic	false
CBR	CD1	ILE- 184	3.65	0	Hydrophobic	false
CAO	CD1	ILE- 184	3.79	0	Hydrophobic	false