scPDB - 2pk5 entry

Protein Data Bank Entry:

PDB ID : 2pk5

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2007-04-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Protease
ID:	Q9J2P7_9HIV1
AC:	Q9J2P7
Organism:	Human immunodeficiency virus 1
Reign:	Viruses
TaxID:	11676
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	44 %
B	56 %

Ligand binding site composition:

B-Factor:	20.251
Number of residues:	50
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.109	951.750

% Hydrophobic	% Polar
46.10	53.90
According to VolSite

Ligand :

HET Code:	075
Formula:	C40H45N5O9S2
Molecular weight:	803.943 g/mol
DrugBank ID:	-
Buried Surface Area:	69.98 %
Polar Surface area:	238 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	5
Rings:	6
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
14.0246	-21.451	-16.2368

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
C23	CD2	LEU- 23	3.98	0	Hydrophobic	false
O3	OD1	ASP- 25	2.73	148.19	H-Bond (Protein Donor)	false
O1	OD1	ASP- 25	3.11	122.3	H-Bond (Protein Donor)	false
O1	OD2	ASP- 25	2.96	127.92	H-Bond (Ligand Donor)	false
O1	OD1	ASP- 25	2.61	153.87	H-Bond (Ligand Donor)	false
N2	O	GLY- 27	3.15	158.56	H-Bond (Ligand Donor)	false
N4	O	GLY- 27	3.47	143.76	H-Bond (Ligand Donor)	false
C34	CB	ALA- 28	3.6	0	Hydrophobic	false
O2	N	ASP- 29	2.87	160.06	H-Bond (Protein Donor)	false
O7	N	ASP- 29	3.02	171.39	H-Bond (Protein Donor)	false
C39	CB	ASP- 29	4.39	0	Hydrophobic	false
O8	N	ASP- 30	2.91	160.55	H-Bond (Protein Donor)	false
C37	CB	ASP- 30	3.64	0	Hydrophobic	false
C38	CG1	VAL- 32	3.61	0	Hydrophobic	false
C11	CB	ILE- 47	4.45	0	Hydrophobic	false
C28	CG2	ILE- 47	3.83	0	Hydrophobic	false
C39	CB	ILE- 47	4.07	0	Hydrophobic	false
C37	CD1	ILE- 47	3.89	0	Hydrophobic	false
N1	O	GLY- 48	2.91	152.41	H-Bond (Ligand Donor)	false
C11	CD1	ILE- 50	4.08	0	Hydrophobic	false
C27	CB	ILE- 50	4.3	0	Hydrophobic	false
C26	CD1	ILE- 50	4.39	0	Hydrophobic	false
S1	CG1	ILE- 50	4.12	0	Hydrophobic	false
C33	CG1	ILE- 50	4.41	0	Hydrophobic	false
C34	CD1	ILE- 50	4.39	0	Hydrophobic	false
C1	CG	PRO- 81	4	0	Hydrophobic	false
C30	CG	PRO- 81	4.5	0	Hydrophobic	false
C3	CB	PRO- 81	3.84	0	Hydrophobic	false
C25	CG	PRO- 81	3.55	0	Hydrophobic	false
C23	CB	VAL- 82	4.49	0	Hydrophobic	false
C29	CB	VAL- 82	4.2	0	Hydrophobic	false
C30	CG2	VAL- 82	4.42	0	Hydrophobic	false
C24	CG2	VAL- 82	3.42	0	Hydrophobic	false
C7	CG2	VAL- 82	3.92	0	Hydrophobic	false
C29	CG2	ILE- 84	3.74	0	Hydrophobic	false
S1	CG2	ILE- 84	4.48	0	Hydrophobic	false
C34	CG2	ILE- 84	3.96	0	Hydrophobic	false
C22	CD1	ILE- 84	3.84	0	Hydrophobic	false