scPDB - 2i4d entry

Protein Data Bank Entry:

PDB ID : 2i4d

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2006-08-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Protease
ID:	Q5RZ08_9HIV1
AC:	Q5RZ08
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:	14.458
Number of residues:	47
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.784	786.375

% Hydrophobic	% Polar
37.34	62.66
According to VolSite

Ligand :

HET Code:	QFI
Formula:	C29H39N2O12PS
Molecular weight:	670.665 g/mol
DrugBank ID:	-
Buried Surface Area:	65.3 %
Polar Surface area:	214.23 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	2
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
14.7957	22.1367	16.3087

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
C11	CD2	LEU- 23	3.92	0	Hydrophobic	false
C15	CB	ALA- 28	4.36	0	Hydrophobic	false
C20	CB	ALA- 28	3.49	0	Hydrophobic	false
C26	CB	ASP- 29	3.89	0	Hydrophobic	false
O1	N	ASP- 30	3.23	144.73	H-Bond (Protein Donor)	false
C26	CB	ASP- 30	4.11	0	Hydrophobic	false
C20	CG2	VAL- 32	3.78	0	Hydrophobic	false
C26	CG2	ILE- 47	3.83	0	Hydrophobic	false
C22	CB	ILE- 47	4.3	0	Hydrophobic	false
C5	CD1	ILE- 50	4.01	0	Hydrophobic	false
C41	CG	PRO- 81	4.17	0	Hydrophobic	false
C12	CG	PRO- 81	3.57	0	Hydrophobic	false
C14	CG1	VAL- 82	3.43	0	Hydrophobic	false
C19	CD1	ILE- 84	4.3	0	Hydrophobic	false
C8	CD1	ILE- 84	3.87	0	Hydrophobic	false
O6	OD1	ASP- 225	2.76	157.4	H-Bond (Protein Donor)	false
N1	O	GLY- 227	3.25	154.97	H-Bond (Ligand Donor)	false
C3	CB	ALA- 228	3.53	0	Hydrophobic	false
C27	CB	ASP- 229	4	0	Hydrophobic	false
C2	CB	ASP- 229	4.45	0	Hydrophobic	false
O9	N	ASP- 229	2.89	167.91	H-Bond (Protein Donor)	false
O	N	ASP- 230	3.07	164.48	H-Bond (Protein Donor)	false
C3	CG2	VAL- 232	4.16	0	Hydrophobic	false
C10	CB	ILE- 250	4.32	0	Hydrophobic	false
C18	CD1	ILE- 250	4.05	0	Hydrophobic	false
C25	CG	PRO- 281	3.45	0	Hydrophobic	false
C25	CG1	VAL- 282	4.49	0	Hydrophobic	false
C24	CD1	ILE- 284	4.15	0	Hydrophobic	false
C3	CD1	ILE- 284	4.22	0	Hydrophobic	false