scPDB - 2bqv entry

Protein Data Bank Entry:

PDB ID : 2bqv

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2005-04-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Protease
ID:	O92139_9HIV1
AC:	O92139
Organism:	Human immunodeficiency virus 1
Reign:	Viruses
TaxID:	11676
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.100
Number of residues:	39
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.053	968.625

% Hydrophobic	% Polar
43.55	56.45
According to VolSite

Ligand :

HET Code:	A1A
Formula:	C33H40N4O6
Molecular weight:	588.694 g/mol
DrugBank ID:	-
Buried Surface Area:	66.55 %
Polar Surface area:	140.22 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	5
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
13.3498	23.2311	5.99333

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
C34	CD2	LEU- 23	3.99	0	Hydrophobic	false
C32	CD2	LEU- 23	4.34	0	Hydrophobic	false
N12	O	GLY- 27	3.45	174.7	H-Bond (Ligand Donor)	false
O60	O	GLY- 27	3.33	154.91	H-Bond (Ligand Donor)	false
C53	CB	ALA- 28	3.76	0	Hydrophobic	false
O60	N	ASP- 29	3.13	160.17	H-Bond (Protein Donor)	false
C58	CB	ASP- 29	4.46	0	Hydrophobic	false
C56	CB	ASP- 30	3.73	0	Hydrophobic	false
C54	CG1	VAL- 32	3.62	0	Hydrophobic	false
C55	CD1	ILE- 47	3.99	0	Hydrophobic	false
C28	CG1	ILE- 50	4.08	0	Hydrophobic	false
C44	CG1	ILE- 50	4.03	0	Hydrophobic	false
C36	CB	PRO- 81	4.24	0	Hydrophobic	false
C37	CG	PRO- 81	4.41	0	Hydrophobic	false
C35	CG1	VAL- 82	3.67	0	Hydrophobic	false
C33	CD1	ILE- 84	3.91	0	Hydrophobic	false
C24	CD2	LEU- 123	3.83	0	Hydrophobic	false
O6	OD2	ASP- 125	3.05	170.96	H-Bond (Ligand Donor)	false
C44	CB	ALA- 128	3.81	0	Hydrophobic	false
O3	N	ASP- 129	3.25	157.61	H-Bond (Protein Donor)	false
C44	CG1	VAL- 132	4.27	0	Hydrophobic	false
C43	CD1	ILE- 147	4.21	0	Hydrophobic	false
N1	O	GLY- 148	3.15	153.68	H-Bond (Ligand Donor)	false
C52	CD1	ILE- 150	4.43	0	Hydrophobic	false
C53	CG2	ILE- 150	4.43	0	Hydrophobic	false
C38	CG2	ILE- 150	3.79	0	Hydrophobic	false
C26	CB	PRO- 181	4.18	0	Hydrophobic	false
C27	CG	PRO- 181	3.92	0	Hydrophobic	false
C25	CG2	VAL- 182	3.54	0	Hydrophobic	false
C44	CD1	ILE- 184	3.71	0	Hydrophobic	false
C23	CD1	ILE- 184	3.77	0	Hydrophobic	false