scPDB - 3kfn entry

Protein Data Bank Entry:

PDB ID : 3kfn

Resolution :1.770 Å

Experimental Method : X-ray

Deposition Date : 2009-10-27

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_HV1Z2
AC:	P12499
Organism:	Human immunodeficiency virus type 1 group M subtype D
Reign:	Viruses
TaxID:	11683
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	28.191
Number of residues:	48
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.688	789.750

% Hydrophobic	% Polar
38.03	61.97
According to VolSite

Ligand :

HET Code:	3TL
Formula:	C50H64N6O10
Molecular weight:	909.077 g/mol
DrugBank ID:	-
Buried Surface Area:	57.93 %
Polar Surface area:	233.51 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	8
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	4
Rotatable Bonds:	25

Mass center Coordinates

X	Y	Z
12.4832	21.7429	16.9168

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
C9	CD2	LEU- 23	4.17	0	Hydrophobic	false
C55	CD2	LEU- 23	3.6	0	Hydrophobic	false
O51	OD2	ASP- 25	3.04	141.37	H-Bond (Protein Donor)	false
O51	OD2	ASP- 25	2.84	142.43	H-Bond (Ligand Donor)	false
O51	OD1	ASP- 25	2.72	138.54	H-Bond (Ligand Donor)	false
N1	O	GLY- 27	2.81	172.59	H-Bond (Ligand Donor)	false
N51	O	GLY- 27	3.11	145.4	H-Bond (Ligand Donor)	false
CG2	CB	ALA- 28	3.81	0	Hydrophobic	false
CG6	CB	ALA- 28	3.61	0	Hydrophobic	false
O4	N	ASP- 29	2.59	160.08	H-Bond (Protein Donor)	false
O54	N	ASP- 29	2.7	164.99	H-Bond (Protein Donor)	false
C20	CB	ASP- 29	4.13	0	Hydrophobic	false
C70	CB	ASP- 29	4.35	0	Hydrophobic	false
CG2	CG2	VAL- 32	3.87	0	Hydrophobic	false
CG1	CG2	VAL- 32	4.47	0	Hydrophobic	false
CG5	CG2	VAL- 32	4.04	0	Hydrophobic	false
CG5	CD1	ILE- 47	4.09	0	Hydrophobic	false
CG2	CD1	ILE- 47	4	0	Hydrophobic	false
N2	O	GLY- 48	3.08	163.1	H-Bond (Ligand Donor)	false
N52	O	GLY- 48	2.84	165.37	H-Bond (Ligand Donor)	false
C59	CG1	ILE- 50	4.27	0	Hydrophobic	false
CG1	CG1	ILE- 50	3.54	0	Hydrophobic	false
C63	CB	PRO- 81	3.71	0	Hydrophobic	false
C14	CB	PRO- 81	3.58	0	Hydrophobic	false
C15	CG	PRO- 81	3.59	0	Hydrophobic	false
C6	CG	PRO- 81	3.84	0	Hydrophobic	false
C58	CG	PRO- 81	3.73	0	Hydrophobic	false
C64	CG	PRO- 81	3.77	0	Hydrophobic	false
C56	CG1	VAL- 82	3.63	0	Hydrophobic	false
C9	CG1	VAL- 82	3.49	0	Hydrophobic	false
CG1	CD1	ILE- 84	3.8	0	Hydrophobic	false
CG6	CD1	ILE- 84	3.46	0	Hydrophobic	false
C3	CD1	ILE- 84	3.59	0	Hydrophobic	false
C54	CD1	ILE- 84	3.93	0	Hydrophobic	false