scPDB - 1b6m entry

Protein Data Bank Entry:

PDB ID : 1b6m

Resolution :1.850 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:	16.736
Number of residues:	39
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.653	749.250

% Hydrophobic	% Polar
38.29	61.71
According to VolSite

Ligand :

HET Code:	PI6
Formula:	C33H49N4O6
Molecular weight:	597.765 g/mol
DrugBank ID:	-
Buried Surface Area:	63.59 %
Polar Surface area:	142.6 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	5
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
5.36363	-2.31081	14.784

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
CD21	CD2	LEU- 23	3.74	0	Hydrophobic	false
N1	OD2	ASP- 25	2.66	156.01	H-Bond (Ligand Donor)	false
N1	OD1	ASP- 25	3.37	145.28	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 25	2.66	0	Ionic (Ligand Cationic)	false
N1	OD1	ASP- 25	3.37	0	Ionic (Ligand Cationic)	false
N	O	GLY- 27	3.15	146.86	H-Bond (Ligand Donor)	false
C1	CB	ALA- 28	4.01	0	Hydrophobic	false
C2	CB	ASP- 30	4.23	0	Hydrophobic	false
C1	CG2	VAL- 32	4.09	0	Hydrophobic	false
C2	CG2	VAL- 32	4.21	0	Hydrophobic	false
C3	CD1	ILE- 47	4.15	0	Hydrophobic	false
CD2	CG1	ILE- 50	4.37	0	Hydrophobic	false
CD12	CG1	ILE- 50	3.72	0	Hydrophobic	false
CE11	CG	PRO- 81	3.54	0	Hydrophobic	false
CE21	CG2	VAL- 82	3.63	0	Hydrophobic	false
C1	CD1	ILE- 84	4.13	0	Hydrophobic	false
CB1	CD1	ILE- 84	3.72	0	Hydrophobic	false
CB	CD2	LEU- 123	4.07	0	Hydrophobic	false
OXT	OD2	ASP- 125	2.59	163.59	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 125	3.08	165.81	H-Bond (Ligand Donor)	false
N1	OD1	ASP- 125	3.62	0	Ionic (Ligand Cationic)	false
N1	OD2	ASP- 125	3.08	0	Ionic (Ligand Cationic)	false
N2	O	GLY- 127	3.06	154.79	H-Bond (Ligand Donor)	false
CB2	CB	ALA- 128	3.84	0	Hydrophobic	false
O3	N	ASP- 129	2.93	173.6	H-Bond (Protein Donor)	false
CD12	CG2	VAL- 132	3.36	0	Hydrophobic	false
CG2	CD1	ILE- 147	4.16	0	Hydrophobic	false
CD12	CD1	ILE- 147	4.42	0	Hydrophobic	false
N3	O	GLY- 148	2.86	158.43	H-Bond (Ligand Donor)	false
C1	CG1	ILE- 150	4.32	0	Hydrophobic	false
C3	CG2	ILE- 150	4.02	0	Hydrophobic	false
CD11	CD1	ILE- 150	3.61	0	Hydrophobic	false
CE2	CG	PRO- 181	3.66	0	Hydrophobic	false
CG	CG2	VAL- 182	4	0	Hydrophobic	false
CB	CD1	ILE- 184	4.03	0	Hydrophobic	false
CD12	CD1	ILE- 184	3.67	0	Hydrophobic	false