scPDB - 1b6k entry

Protein Data Bank Entry:

PDB ID : 1b6k

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	48 %
B	52 %

Ligand binding site composition:

B-Factor:	11.512
Number of residues:	40
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.878	769.500

% Hydrophobic	% Polar
44.74	55.26
According to VolSite

Ligand :

HET Code:	PI5
Formula:	C37H54N5O7
Molecular weight:	680.854 g/mol
DrugBank ID:	-
Buried Surface Area:	60.88 %
Polar Surface area:	173.9 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	6
Rings:	5
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
5.36608	-1.42082	14.0846

Binding mode :

What is Poseview ?

2D View
3D View

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
C30	CD2	LEU- 23	3.79	0	Hydrophobic	false
N26	OD2	ASP- 25	2.71	159.06	H-Bond (Ligand Donor)	false
N26	OD1	ASP- 25	3.42	143.71	H-Bond (Ligand Donor)	false
N26	OD2	ASP- 25	2.71	0	Ionic (Ligand Cationic)	false
N26	OD1	ASP- 25	3.42	0	Ionic (Ligand Cationic)	false
N13	O	GLY- 27	2.97	147.2	H-Bond (Ligand Donor)	false
C9	CB	ALA- 28	3.93	0	Hydrophobic	false
O4	N	ASP- 29	2.89	163.2	H-Bond (Protein Donor)	false
C10	CB	ASP- 30	4.38	0	Hydrophobic	false
C9	CG2	VAL- 32	4.31	0	Hydrophobic	false
C10	CG2	VAL- 32	3.99	0	Hydrophobic	false
C10	CD1	ILE- 47	4.19	0	Hydrophobic	false
C46	CD1	ILE- 50	4.15	0	Hydrophobic	false
C33	CG	PRO- 81	3.27	0	Hydrophobic	false
C31	CG1	VAL- 82	3.71	0	Hydrophobic	false
C9	CD1	ILE- 84	3.93	0	Hydrophobic	false
C28	CD1	ILE- 84	3.72	0	Hydrophobic	false
C15	CD2	LEU- 123	3.96	0	Hydrophobic	false
C18	CD2	LEU- 123	4.31	0	Hydrophobic	false
O24	OD2	ASP- 125	2.53	165.27	H-Bond (Ligand Donor)	false
N26	OD2	ASP- 125	3.16	166.94	H-Bond (Ligand Donor)	false
N26	OD1	ASP- 125	3.55	0	Ionic (Ligand Cationic)	false
N26	OD2	ASP- 125	3.16	0	Ionic (Ligand Cationic)	false
N39	O	GLY- 127	3.06	156.9	H-Bond (Ligand Donor)	false
C43	CB	ALA- 128	3.73	0	Hydrophobic	false
O42	N	ASP- 129	2.87	170.21	H-Bond (Protein Donor)	false
C45	CG2	VAL- 132	4.33	0	Hydrophobic	false
C46	CG2	VAL- 132	4.14	0	Hydrophobic	false
C45	CD1	ILE- 147	3.98	0	Hydrophobic	false
N47	O	GLY- 148	3.03	159.17	H-Bond (Ligand Donor)	false
C9	CD1	ILE- 150	4.19	0	Hydrophobic	false
C20	CG1	VAL- 182	4.04	0	Hydrophobic	false
C16	CG2	VAL- 182	3.84	0	Hydrophobic	false
C15	CD1	ILE- 184	3.92	0	Hydrophobic	false
C46	CD1	ILE- 184	4.11	0	Hydrophobic	false