scPDB - 1b6l entry

Protein Data Bank Entry:

PDB ID : 1b6l

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 1999-01-17

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	50 %
B	50 %

Ligand binding site composition:

B-Factor:	14.627
Number of residues:	41
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.641	658.125

% Hydrophobic	% Polar
41.03	58.97
According to VolSite

Ligand :

HET Code:	PI4
Formula:	C28H44N5O6
Molecular weight:	546.679 g/mol
DrugBank ID:	-
Buried Surface Area:	66.52 %
Polar Surface area:	164.28 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	6
Rings:	4
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
5.42969	-0.52141	13.4932

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
O25	OD1	ASP- 25	2.57	158.25	H-Bond (Protein Donor)	false
N13	O	GLY- 27	3.35	162.18	H-Bond (Ligand Donor)	false
C9	CB	ALA- 28	4.02	0	Hydrophobic	false
O11	N	ASP- 30	2.77	163.74	H-Bond (Protein Donor)	false
N12	OD2	ASP- 30	3.4	147.3	H-Bond (Ligand Donor)	false
N5	O	GLY- 48	2.8	147.47	H-Bond (Ligand Donor)	false
N12	O	GLY- 48	3.45	164.02	H-Bond (Ligand Donor)	false
C36	CG1	ILE- 50	4.49	0	Hydrophobic	false
C38	CG2	ILE- 50	3.68	0	Hydrophobic	false
C19	CD1	ILE- 50	4.2	0	Hydrophobic	false
C31	CG1	VAL- 82	3.72	0	Hydrophobic	false
C9	CD1	ILE- 84	4.42	0	Hydrophobic	false
C31	CG2	ILE- 84	3.9	0	Hydrophobic	false
C17	CD2	LEU- 123	4	0	Hydrophobic	false
O25	OD2	ASP- 125	2.63	149.71	H-Bond (Ligand Donor)	false
C36	CB	ALA- 128	4.16	0	Hydrophobic	false
C37	CB	ALA- 128	4.19	0	Hydrophobic	false
C37	CB	ASP- 130	4.36	0	Hydrophobic	false
C36	CG2	VAL- 132	4.03	0	Hydrophobic	false
C37	CG2	VAL- 132	4.05	0	Hydrophobic	false
C38	CD1	ILE- 147	3.81	0	Hydrophobic	false
C9	CD1	ILE- 150	3.83	0	Hydrophobic	false
C20	CG	PRO- 181	4.21	0	Hydrophobic	false
C18	CG1	VAL- 182	3.69	0	Hydrophobic	false
C21	CG1	VAL- 182	3.7	0	Hydrophobic	false
C36	CD1	ILE- 184	3.72	0	Hydrophobic	false
C16	CD1	ILE- 184	3.61	0	Hydrophobic	false
N12	O	HOH- 341	3.43	136.95	H-Bond (Ligand Donor)	false