scPDB - 4kko entry

Protein Data Bank Entry:

PDB ID : 4kko

Resolution :2.890 Å

Experimental Method : X-ray

Deposition Date : 2013-05-06

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	88 %
B	12 %

Ligand binding site composition:

B-Factor:	48.776
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.568	415.125

% Hydrophobic	% Polar
73.98	26.02
According to VolSite

Ligand :

HET Code:	1RE
Formula:	C22H31N6O4
Molecular weight:	443.519 g/mol
DrugBank ID:	-
Buried Surface Area:	59.8 %
Polar Surface area:	115.85 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
33.3005	-24.7829	141.896

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
CAB	CD1	LEU- 100	3.76	0	Hydrophobic	false
CBA	CB	LEU- 100	3.92	0	Hydrophobic	false
CAI	CD1	LEU- 100	3.65	0	Hydrophobic	false
NAR	N	LYS- 101	3.33	161.81	H-Bond (Protein Donor)	false
CAM	CB	LYS- 101	4.48	0	Hydrophobic	false
CBA	CG	LYS- 103	4.19	0	Hydrophobic	false
CAJ	CG1	VAL- 106	3.77	0	Hydrophobic	false
CAZ	CG2	VAL- 106	3.8	0	Hydrophobic	false
NBF	OE1	GLU- 138	3.94	0	Ionic (Ligand Cationic)	false
CAA	CG2	VAL- 179	3.98	0	Hydrophobic	false
CAB	CD2	TYR- 181	3.88	0	Hydrophobic	false
CAA	CB	TYR- 181	3.58	0	Hydrophobic	false
CAC	CE2	TYR- 188	3.58	0	Hydrophobic	false
CAJ	CD2	TYR- 188	3.46	0	Hydrophobic	false
CAC	CD2	TRP- 229	4.3	0	Hydrophobic	false
CAB	CZ3	TRP- 229	4.3	0	Hydrophobic	false
CAC	CD2	LEU- 234	3.68	0	Hydrophobic	false
CAB	CD2	LEU- 234	4.45	0	Hydrophobic	false
CAG	CE1	TYR- 318	3.46	0	Hydrophobic	false