scPDB - 3dok entry

Protein Data Bank Entry:

PDB ID : 3dok

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2008-07-04

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:	A7YKL0_9HIV1
AC:	A7YKL0
Organism:	Human immunodeficiency virus 1
Reign:	Viruses
TaxID:	11676
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	63.001
Number of residues:	35
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.396	536.625

% Hydrophobic	% Polar
62.26	37.74
According to VolSite

Ligand :

HET Code:	GWJ
Formula:	C23H17Cl2N3O5S
Molecular weight:	518.369 g/mol
DrugBank ID:	-
Buried Surface Area:	76.38 %
Polar Surface area:	147.72 Å2

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

Mass center Coordinates

X	Y	Z
-4.31015	-34.475	24.044

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
CL1	CB	PRO- 95	4.08	0	Hydrophobic	false
C6	CB	LEU- 100	4.06	0	Hydrophobic	false
C15	CB	LEU- 100	3.86	0	Hydrophobic	false
C1	CD2	LEU- 100	3.8	0	Hydrophobic	false
C9	CD2	LEU- 100	3.43	0	Hydrophobic	false
O3	N	ASN- 103	2.89	162.78	H-Bond (Protein Donor)	false
C6	CB	ASN- 103	4.27	0	Hydrophobic	false
N3	O	LYS- 104	3.33	171.66	H-Bond (Ligand Donor)	false
CL	CG2	VAL- 106	4.35	0	Hydrophobic	false
C22	CG2	VAL- 106	3.42	0	Hydrophobic	false
C21	CB	VAL- 106	3.87	0	Hydrophobic	false
C3	CG2	VAL- 106	3.45	0	Hydrophobic	false
O5	N	VAL- 106	3.26	169.96	H-Bond (Protein Donor)	false
CL	CG1	VAL- 179	3.54	0	Hydrophobic	false
CL	CD2	TYR- 181	4.01	0	Hydrophobic	false
CL1	CD1	TYR- 181	4.12	0	Hydrophobic	false
C3	CB	TYR- 188	4.06	0	Hydrophobic	false
CL	CB	TYR- 188	4.05	0	Hydrophobic	false
CL1	CD1	TYR- 188	3.6	0	Hydrophobic	false
C11	CD1	TYR- 188	3.26	0	Hydrophobic	false
C10	CB	TYR- 188	4.14	0	Hydrophobic	false
C19	CB	PRO- 225	4.48	0	Hydrophobic	false
C13	CB	PHE- 227	4.4	0	Hydrophobic	false
C23	CD2	PHE- 227	3.81	0	Hydrophobic	false
CL1	CZ2	TRP- 229	3.57	0	Hydrophobic	false
C23	CB	LEU- 234	3.98	0	Hydrophobic	false
C12	CD2	LEU- 234	4.14	0	Hydrophobic	false
C8	CD2	LEU- 234	3.79	0	Hydrophobic	false
C19	CG	PRO- 236	3.71	0	Hydrophobic	false
C15	CD1	TYR- 318	3.32	0	Hydrophobic	false