scPDB - 1kzk entry

Protein Data Bank Entry:

PDB ID : 1kzk

Resolution :1.090 Å

Experimental Method : X-ray

Deposition Date : 2002-02-06

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_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	49 %
B	51 %

Ligand binding site composition:

B-Factor:	10.354
Number of residues:	43
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.089	769.500

% Hydrophobic	% Polar
48.25	51.75
According to VolSite

Ligand :

HET Code:	JE2
Formula:	C32H37N3O5S
Molecular weight:	575.718 g/mol
DrugBank ID:	DB02668
Buried Surface Area:	73.49 %
Polar Surface area:	144.27 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	4
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
19.8588	-1.74	16.8945

Binding mode :

What is Poseview ?

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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
C15	CD2	LEU- 23	3.77	0	Hydrophobic	false
C28	CD2	LEU- 23	3.51	0	Hydrophobic	false
O23	OD2	ASP- 25	2.67	155.62	H-Bond (Protein Donor)	false
O21	OD1	ASP- 25	2.62	161.48	H-Bond (Ligand Donor)	false
O21	OD2	ASP- 25	3.26	130.27	H-Bond (Ligand Donor)	false
N11	O	GLY- 27	3.03	158.66	H-Bond (Ligand Donor)	false
C8	CB	ALA- 28	3.76	0	Hydrophobic	false
C7	CB	ALA- 28	4.01	0	Hydrophobic	false
C36	CB	ALA- 28	3.85	0	Hydrophobic	false
C3	CB	ASP- 29	3.68	0	Hydrophobic	false
C1	CB	ASP- 30	4.42	0	Hydrophobic	false
C38	CB	ASP- 30	3.67	0	Hydrophobic	false
O2	OD2	ASP- 30	2.68	169.13	H-Bond (Ligand Donor)	false
C8	CG2	VAL- 32	3.92	0	Hydrophobic	false
C37	CG1	VAL- 32	3.77	0	Hydrophobic	false
C1	CD1	ILE- 47	4.41	0	Hydrophobic	false
C8	CD1	ILE- 47	4.39	0	Hydrophobic	false
C39	CG2	ILE- 47	3.76	0	Hydrophobic	false
C40	CB	ILE- 47	3.69	0	Hydrophobic	false
C37	CD1	ILE- 47	4	0	Hydrophobic	false
C8	CG1	ILE- 50	4.14	0	Hydrophobic	false
C19	CB	ILE- 50	4.27	0	Hydrophobic	false
S26	CG1	ILE- 50	4.17	0	Hydrophobic	false
C41	CD1	ILE- 50	4.16	0	Hydrophobic	false
C38	CD1	LEU- 76	4.14	0	Hydrophobic	false
C29	CG	PRO- 81	4.18	0	Hydrophobic	false
S26	CG	PRO- 81	3.69	0	Hydrophobic	false
C17	CG	PRO- 81	3.72	0	Hydrophobic	false
C28	CG2	VAL- 82	4.04	0	Hydrophobic	false
C16	CG2	VAL- 82	3.63	0	Hydrophobic	false
C8	CD1	ILE- 84	4.31	0	Hydrophobic	false
S26	CD1	ILE- 84	3.97	0	Hydrophobic	false
C41	CD1	ILE- 84	4.1	0	Hydrophobic	false
C14	CD1	ILE- 84	3.74	0	Hydrophobic	false
N33	O	HOH- 1040	3.04	164.78	H-Bond (Ligand Donor)	false