scPDB - 1b6p entry

Protein Data Bank Entry:

PDB ID : 1b6p

Resolution :2.000 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	49 %
B	51 %

Ligand binding site composition:

B-Factor:	11.688
Number of residues:	39
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.819	702.000

% Hydrophobic	% Polar
44.71	55.29
According to VolSite

Ligand :

HET Code:	PI7
Formula:	C36H54N5O7
Molecular weight:	668.843 g/mol
DrugBank ID:	-
Buried Surface Area:	64.34 %
Polar Surface area:	182.69 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	7
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
5.29771	-1.699	14.2468

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
C27	CD2	LEU- 23	4.47	0	Hydrophobic	false
C29	CD2	LEU- 23	3.76	0	Hydrophobic	false
N25	OD2	ASP- 25	2.79	163.29	H-Bond (Ligand Donor)	false
N25	OD1	ASP- 25	3.49	141.3	H-Bond (Ligand Donor)	false
N25	OD2	ASP- 25	2.79	0	Ionic (Ligand Cationic)	false
N25	OD1	ASP- 25	3.49	0	Ionic (Ligand Cationic)	false
N12	O	GLY- 27	2.89	144.79	H-Bond (Ligand Donor)	false
C10	CB	ALA- 28	3.84	0	Hydrophobic	false
C2	CB	ASP- 29	4.32	0	Hydrophobic	false
O4	N	ASP- 29	3.16	162.58	H-Bond (Protein Donor)	false
C11	CB	ASP- 30	4.39	0	Hydrophobic	false
C10	CG2	VAL- 32	4.41	0	Hydrophobic	false
C11	CG2	VAL- 32	3.68	0	Hydrophobic	false
C11	CD1	ILE- 47	4.02	0	Hydrophobic	false
N5	O	GLY- 48	3	148.52	H-Bond (Ligand Donor)	false
C16	CG1	ILE- 50	4.47	0	Hydrophobic	false
C43	CG1	ILE- 50	4.21	0	Hydrophobic	false
C32	CG	PRO- 81	3.37	0	Hydrophobic	false
C30	CG1	VAL- 82	3.52	0	Hydrophobic	false
C10	CD1	ILE- 84	4.08	0	Hydrophobic	false
C27	CD1	ILE- 84	3.65	0	Hydrophobic	false
C14	CD2	LEU- 123	4.35	0	Hydrophobic	false
C17	CD2	LEU- 123	4.02	0	Hydrophobic	false
O23	OD2	ASP- 125	2.56	152.74	H-Bond (Ligand Donor)	false
N25	OD1	ASP- 125	3.76	0	Ionic (Ligand Cationic)	false
N25	OD2	ASP- 125	3.53	0	Ionic (Ligand Cationic)	false
N38	O	GLY- 127	3.06	156	H-Bond (Ligand Donor)	false
C45	CB	ALA- 128	3.94	0	Hydrophobic	false
O41	N	ASP- 129	2.98	167.67	H-Bond (Protein Donor)	false
C45	CG2	VAL- 132	3.43	0	Hydrophobic	false
C44	CB	ILE- 147	4.09	0	Hydrophobic	false
N46	O	GLY- 148	2.79	157.69	H-Bond (Ligand Donor)	false
C31	CD1	ILE- 150	4.4	0	Hydrophobic	false
C10	CG1	ILE- 150	3.56	0	Hydrophobic	false
C18	CG	PRO- 181	3.67	0	Hydrophobic	false
C17	CG1	VAL- 182	3.86	0	Hydrophobic	false
C14	CD1	ILE- 184	3.98	0	Hydrophobic	false
C45	CD1	ILE- 184	3.4	0	Hydrophobic	false