scPDB - 4ko0 entry

Protein Data Bank Entry:

PDB ID : 4ko0

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2013-05-10

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_HV1B1
AC:	P03366
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11678
EC Number:	2.7.7.49

Chains:

Chain Name:	Percentage of Residues within binding site
A	96 %
B	4 %

Ligand binding site composition:

B-Factor:	47.108
Number of residues:	27
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.759	371.250

% Hydrophobic	% Polar
80.91	19.09
According to VolSite

Ligand :

HET Code:	JLJ
Formula:	C17H18N4O2
Molecular weight:	310.350 g/mol
DrugBank ID:	-
Buried Surface Area:	80.75 %
Polar Surface area:	80.06 Å2

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

Mass center Coordinates

X	Y	Z
50.8749	-27.7402	35.5363

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
C45	CG	PRO- 95	4.33	0	Hydrophobic	false
C14	CD2	LEU- 100	4.27	0	Hydrophobic	false
C23	CB	LEU- 100	4.02	0	Hydrophobic	false
C45	CD1	LEU- 100	3.99	0	Hydrophobic	false
C22	CD1	LEU- 100	3.93	0	Hydrophobic	false
N16	N	LYS- 101	3.13	169.85	H-Bond (Protein Donor)	false
N19	O	LYS- 101	2.64	169.12	H-Bond (Ligand Donor)	false
C24	CG	LYS- 103	3.72	0	Hydrophobic	false
C41	CG1	VAL- 106	4.07	0	Hydrophobic	false
C20	CG2	VAL- 106	3.64	0	Hydrophobic	false
C14	CG2	VAL- 179	3.88	0	Hydrophobic	false
C18	CG2	VAL- 179	4.16	0	Hydrophobic	false
C18	CB	TYR- 181	3.58	0	Hydrophobic	false
C44	CD2	TYR- 181	4.18	0	Hydrophobic	false
C45	CE2	TYR- 181	3.8	0	Hydrophobic	false
C18	CB	TYR- 188	4	0	Hydrophobic	false
C41	CD1	TYR- 188	3.63	0	Hydrophobic	false
C44	CE1	TYR- 188	3.73	0	Hydrophobic	false
C44	CD2	TRP- 229	3.95	0	Hydrophobic	false
C45	CH2	TRP- 229	3.88	0	Hydrophobic	false
C41	CD1	LEU- 234	4.31	0	Hydrophobic	false
C44	CD1	LEU- 234	3.52	0	Hydrophobic	false
C45	CD1	LEU- 234	4.02	0	Hydrophobic	false