scPDB - 2q55 entry

Protein Data Bank Entry:

PDB ID : 2q55

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2007-05-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Protease
ID:	O38719_9HIV1
AC:	O38719
Organism:	Human immunodeficiency virus 1
Reign:	Viruses
TaxID:	11676
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	45 %
B	55 %

Ligand binding site composition:

B-Factor:	17.558
Number of residues:	44
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.775	658.125

% Hydrophobic	% Polar
44.62	55.38
According to VolSite

Ligand :

HET Code:	MU0
Formula:	C37H45N5O6
Molecular weight:	655.783 g/mol
DrugBank ID:	-
Buried Surface Area:	69.31 %
Polar Surface area:	140.31 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	4
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
19.597	30.814	13.8127

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
C22	CD1	LEU- 23	4.17	0	Hydrophobic	false
O4	OD1	ASP- 25	2.84	132.75	H-Bond (Ligand Donor)	false
O4	OD2	ASP- 25	2.98	154.74	H-Bond (Ligand Donor)	false
N3	O	GLY- 27	2.95	153.11	H-Bond (Ligand Donor)	false
C27	CB	ALA- 28	4.49	0	Hydrophobic	false
C14	CB	ALA- 28	3.84	0	Hydrophobic	false
O1	N	ASP- 29	2.83	172.22	H-Bond (Protein Donor)	false
N2	OD2	ASP- 29	3.11	162.54	H-Bond (Ligand Donor)	false
O30	N	ASP- 30	3.02	165.35	H-Bond (Protein Donor)	false
C15	CB	ASP- 30	4.23	0	Hydrophobic	false
C38	CB	ASP- 30	3.86	0	Hydrophobic	false
C38	CG2	VAL- 32	4.41	0	Hydrophobic	false
C15	CG2	VAL- 32	3.79	0	Hydrophobic	false
C36	CG2	ILE- 47	3.55	0	Hydrophobic	false
C15	CD1	ILE- 47	4.28	0	Hydrophobic	false
C39	CB	ILE- 47	4.04	0	Hydrophobic	false
C37	CB	ILE- 47	3.54	0	Hydrophobic	false
C35	CB	ILE- 47	4.09	0	Hydrophobic	false
C27	CD1	ILE- 50	4.06	0	Hydrophobic	false
C21	CG1	ILE- 50	4.22	0	Hydrophobic	false
C14	CD1	ILE- 50	4.02	0	Hydrophobic	false
C37	CD1	LEU- 76	4.03	0	Hydrophobic	false
C8	CG	PRO- 81	3.76	0	Hydrophobic	false
C16	CG	PRO- 81	3.86	0	Hydrophobic	false
C6	CG1	VAL- 82	3.79	0	Hydrophobic	false
C21	CG1	VAL- 82	3.36	0	Hydrophobic	false
C27	CD1	ILE- 84	4.03	0	Hydrophobic	false
C23	CD1	ILE- 84	4.23	0	Hydrophobic	false
C14	CD1	ILE- 84	3.8	0	Hydrophobic	false
C22	CD1	ILE- 84	4.05	0	Hydrophobic	false
C9	CD1	ILE- 84	3.81	0	Hydrophobic	false