scPDB - 2f3k entry

Protein Data Bank Entry:

PDB ID : 2f3k

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2005-11-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Protease
ID:	O38708_9HIV1
AC:	O38708
Organism:	Human immunodeficiency virus 1
Reign:	Viruses
TaxID:	11676
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	48 %
B	52 %

Ligand binding site composition:

B-Factor:	15.148
Number of residues:	44
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.201	830.250

% Hydrophobic	% Polar
48.78	51.22
According to VolSite

Ligand :

HET Code:	RO1
Formula:	C37H54N5O7S
Molecular weight:	712.919 g/mol
DrugBank ID:	-
Buried Surface Area:	66.72 %
Polar Surface area:	173.44 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
19.9997	-3.52782	15.7733

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
C11	CD2	LEU- 23	4.46	0	Hydrophobic	false
C27	CD2	LEU- 23	3.97	0	Hydrophobic	false
O2	OD1	ASP- 25	2.57	162.3	H-Bond (Protein Donor)	false
N4	O	GLY- 27	3.27	154.28	H-Bond (Ligand Donor)	false
C33	CB	ALA- 28	4.19	0	Hydrophobic	false
C22	CB	ALA- 28	3.94	0	Hydrophobic	false
C21	CB	ALA- 28	3.99	0	Hydrophobic	false
C37	CB	ASP- 29	4.47	0	Hydrophobic	false
O4	N	ASP- 29	2.99	158.32	H-Bond (Protein Donor)	false
O6	N	ASP- 30	2.9	160.11	H-Bond (Protein Donor)	false
C37	CB	ASP- 30	4.42	0	Hydrophobic	false
C22	CB	ASP- 30	4.18	0	Hydrophobic	false
C33	CG2	VAL- 32	4.22	0	Hydrophobic	false
C22	CG2	VAL- 32	4.06	0	Hydrophobic	false
C21	CG2	VAL- 32	4.16	0	Hydrophobic	false
C37	CB	ILE- 47	4.22	0	Hydrophobic	false
C34	CB	ILE- 47	4.1	0	Hydrophobic	false
C23	CG2	ILE- 47	3.31	0	Hydrophobic	false
C22	CD1	ILE- 47	3.86	0	Hydrophobic	false
N5	O	GLY- 48	3.39	163.48	H-Bond (Ligand Donor)	false
C33	CD1	ILE- 50	3.69	0	Hydrophobic	false
C34	CD1	ILE- 50	4.28	0	Hydrophobic	false
C23	CG2	ILE- 50	3.91	0	Hydrophobic	false
C20	CG1	ILE- 50	3.97	0	Hydrophobic	false
C18	CG1	ILE- 50	3.48	0	Hydrophobic	false
C4	CB	PRO- 81	3.89	0	Hydrophobic	false
C1	CG	PRO- 81	4.21	0	Hydrophobic	false
C35	CG	PRO- 81	3.73	0	Hydrophobic	false
C20	CG	PRO- 81	3.61	0	Hydrophobic	false
C16	CG2	VAL- 82	4.37	0	Hydrophobic	false
C4	CG2	VAL- 82	4.02	0	Hydrophobic	false
C30	CG2	VAL- 82	4.12	0	Hydrophobic	false
C33	CD1	ILE- 84	4.06	0	Hydrophobic	false
C21	CD1	ILE- 84	3.84	0	Hydrophobic	false
C25	CD1	ILE- 84	4.06	0	Hydrophobic	false
C28	CD1	ILE- 84	3.98	0	Hydrophobic	false
C14	CD1	ILE- 84	3.26	0	Hydrophobic	false