scPDB - 2i4w entry

Protein Data Bank Entry:

PDB ID : 2i4w

Resolution :1.550 Å

Experimental Method : X-ray

Deposition Date : 2006-08-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Protease
ID:	O92139_9HIV1
AC:	O92139
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:	15.588
Number of residues:	46
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.762	776.250

% Hydrophobic	% Polar
39.13	60.87
According to VolSite

Ligand :

HET Code:	KGQ
Formula:	C33H49N2O12PS
Molecular weight:	728.787 g/mol
DrugBank ID:	-
Buried Surface Area:	63.1 %
Polar Surface area:	186.58 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	2
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	20

Mass center Coordinates

X	Y	Z
14.706	21.5916	15.9092

Binding mode :

What is Poseview ?

2D View
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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
C10	CD2	LEU- 23	4.17	0	Hydrophobic	false
O8	OD1	ASP- 25	2.86	137.28	H-Bond (Protein Donor)	false
C20	CB	ALA- 28	4.37	0	Hydrophobic	false
C24	CB	ALA- 28	3.42	0	Hydrophobic	false
C31	CB	ASP- 29	3.7	0	Hydrophobic	false
O5	N	ASP- 30	3.26	139.51	H-Bond (Protein Donor)	false
C31	CB	ASP- 30	4.19	0	Hydrophobic	false
C25	CG2	VAL- 32	3.75	0	Hydrophobic	false
C27	CB	ILE- 47	4.27	0	Hydrophobic	false
C31	CG2	ILE- 47	4.18	0	Hydrophobic	false
C5	CD1	ILE- 50	3.96	0	Hydrophobic	false
C15	CG	PRO- 81	4.27	0	Hydrophobic	false
C16	CB	PRO- 81	4.46	0	Hydrophobic	false
C13	CG	PRO- 81	3.43	0	Hydrophobic	false
C18	CB	PRO- 81	3.43	0	Hydrophobic	false
C14	CG1	VAL- 82	3.35	0	Hydrophobic	false
C11	CD1	ILE- 84	3.73	0	Hydrophobic	false
C30	CD2	LEU- 223	4.37	0	Hydrophobic	false
O8	OD1	ASP- 225	2.66	132.38	H-Bond (Ligand Donor)	false
O8	OD2	ASP- 225	2.87	154.1	H-Bond (Ligand Donor)	false
N	O	GLY- 227	3.3	162.75	H-Bond (Ligand Donor)	false
C3	CB	ALA- 228	3.75	0	Hydrophobic	false
C32	CB	ASP- 229	4.08	0	Hydrophobic	false
C2	CB	ASP- 229	4.3	0	Hydrophobic	false
O11	N	ASP- 229	3.09	155.24	H-Bond (Protein Donor)	false
O4	N	ASP- 230	3.22	170.83	H-Bond (Protein Donor)	false
C3	CG2	VAL- 232	3.89	0	Hydrophobic	false
C	CB	ILE- 247	4.41	0	Hydrophobic	false
C3	CD1	ILE- 247	4.34	0	Hydrophobic	false
C11	CB	ILE- 250	4.31	0	Hydrophobic	false
C23	CD1	ILE- 250	4.22	0	Hydrophobic	false
C18	CZ	PHE- 253	4.26	0	Hydrophobic	false
C19	CE1	PHE- 253	3.46	0	Hydrophobic	false
C30	CG	PRO- 281	4.38	0	Hydrophobic	false
C30	CG2	VAL- 282	3.93	0	Hydrophobic	false
C29	CG2	ILE- 284	3.94	0	Hydrophobic	false
C3	CD1	ILE- 284	4.07	0	Hydrophobic	false