scPDB - 1wbk entry

Protein Data Bank Entry:

PDB ID : 1wbk

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2004-11-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pol protein
ID:	Q8Q3H0_9HIV1
AC:	Q8Q3H0
Organism:	Human immunodeficiency virus 1
Reign:	Viruses
TaxID:	11676
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.474
Number of residues:	45
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.959	830.250

% Hydrophobic	% Polar
45.53	54.47
According to VolSite

Ligand :

HET Code:	568
Formula:	C34H40N2O9
Molecular weight:	620.689 g/mol
DrugBank ID:	DB01887
Buried Surface Area:	67.97 %
Polar Surface area:	166.8 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
13.4732	22.7899	5.37696

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
C19	CD2	LEU- 23	3.7	0	Hydrophobic	false
C41	CD2	LEU- 23	3.68	0	Hydrophobic	false
O21	OD2	ASP- 25	2.71	169.68	H-Bond (Ligand Donor)	false
O23	OD2	ASP- 25	2.78	147.32	H-Bond (Ligand Donor)	false
N8	O	GLY- 27	2.97	164.51	H-Bond (Ligand Donor)	false
N26	O	GLY- 27	3.17	164.92	H-Bond (Ligand Donor)	false
C4	CB	ALA- 28	4.37	0	Hydrophobic	false
C6	CB	ALA- 28	3.91	0	Hydrophobic	false
C33	CB	ALA- 28	3.65	0	Hydrophobic	false
O1	N	ASP- 29	3.12	151.31	H-Bond (Protein Donor)	false
O36	N	ASP- 29	3.2	145.69	H-Bond (Protein Donor)	false
C2	CB	ASP- 29	4.26	0	Hydrophobic	false
C29	CB	ASP- 29	4.1	0	Hydrophobic	false
O36	OD2	ASP- 29	2.91	146.53	H-Bond (Ligand Donor)	false
O7	N	ASP- 30	2.82	140.85	H-Bond (Protein Donor)	false
C34	CB	ASP- 30	3.63	0	Hydrophobic	false
C34	CG2	VAL- 32	3.44	0	Hydrophobic	false
C5	CB	ILE- 47	4.48	0	Hydrophobic	false
C6	CD1	ILE- 47	4.46	0	Hydrophobic	false
C30	CB	ILE- 47	4.32	0	Hydrophobic	false
C35	CG2	ILE- 47	3.94	0	Hydrophobic	false
C34	CD1	ILE- 47	4.04	0	Hydrophobic	false
C22	CD1	ILE- 50	4.19	0	Hydrophobic	false
C15	CD1	ILE- 50	3.95	0	Hydrophobic	false
C34	CD1	LEU- 76	4.41	0	Hydrophobic	false
C16	CB	PRO- 81	3.64	0	Hydrophobic	false
C44	CG	PRO- 81	3.54	0	Hydrophobic	false
C19	CG2	VAL- 82	3.75	0	Hydrophobic	false
C40	CG1	VAL- 82	3.66	0	Hydrophobic	false
C13	CD1	ILE- 84	3.47	0	Hydrophobic	false
C39	CD1	ILE- 84	3.54	0	Hydrophobic	false
O36	O	HOH- 2007	3.21	129.79	H-Bond (Protein Donor)	false