scPDB - 2p3d entry

Protein Data Bank Entry:

PDB ID : 2p3d

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2007-03-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Protease
ID:	Q7SRY5_9HIV1
AC:	Q7SRY5
Organism:	Human immunodeficiency virus 1
Reign:	Viruses
TaxID:	11676
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	53 %
B	47 %

Ligand binding site composition:

B-Factor:	38.490
Number of residues:	47
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.773	756.000

% Hydrophobic	% Polar
41.52	58.48
According to VolSite

Ligand :

HET Code:	3TL
Formula:	C50H64N6O10
Molecular weight:	909.077 g/mol
DrugBank ID:	-
Buried Surface Area:	54.38 %
Polar Surface area:	233.51 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	8
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	4
Rotatable Bonds:	25

Mass center Coordinates

X	Y	Z
7.97332	-13.9227	-0.220515

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
C58	CD2	LEU- 23	4.32	0	Hydrophobic	false
O1	OD1	ASP- 25	3.14	148.75	H-Bond (Ligand Donor)	false
O1	OD2	ASP- 25	2.64	143.16	H-Bond (Ligand Donor)	false
O51	OD2	ASP- 25	2.53	170.2	H-Bond (Ligand Donor)	false
N1	O	GLY- 27	2.94	144.41	H-Bond (Ligand Donor)	false
CG1	CB	ALA- 28	3.75	0	Hydrophobic	false
CG5	CB	ALA- 28	3.52	0	Hydrophobic	false
N4	OD2	ASP- 29	2.6	163.15	H-Bond (Ligand Donor)	false
N54	OD2	ASP- 29	2.78	148.9	H-Bond (Ligand Donor)	false
O4	N	ASP- 29	3.03	166.52	H-Bond (Protein Donor)	false
O54	N	ASP- 29	2.83	158.67	H-Bond (Protein Donor)	false
CG6	CB	ASP- 30	4.33	0	Hydrophobic	false
CG2	CG2	VAL- 32	3.62	0	Hydrophobic	false
CG5	CG2	VAL- 32	3.7	0	Hydrophobic	false
CG6	CG2	ILE- 47	3.74	0	Hydrophobic	false
CA5	CG2	ILE- 47	4.29	0	Hydrophobic	false
CG2	CD1	ILE- 47	3.59	0	Hydrophobic	false
O8	N	GLY- 48	3.4	148.39	H-Bond (Protein Donor)	false
O58	N	GLY- 48	2.84	157.88	H-Bond (Protein Donor)	false
N2	O	GLY- 48	2.71	170.76	H-Bond (Ligand Donor)	false
N52	O	GLY- 48	3.13	167	H-Bond (Ligand Donor)	false
C53	CG1	ILE- 50	3.88	0	Hydrophobic	false
C12	CG1	ILE- 50	3.69	0	Hydrophobic	false
C8	CD1	ILE- 50	3.57	0	Hydrophobic	false
CG5	CG1	ILE- 50	4.18	0	Hydrophobic	false
C14	CE2	PHE- 53	3.09	0	Hydrophobic	false
C6	CB	PRO- 81	4.38	0	Hydrophobic	false
C56	CG	PRO- 81	3.87	0	Hydrophobic	false
C7	CG	PRO- 81	3.26	0	Hydrophobic	false
C57	CB	PRO- 81	3.73	0	Hydrophobic	false
C58	CB	ALA- 82	3.7	0	Hydrophobic	false
CG1	CD1	ILE- 84	3.52	0	Hydrophobic	false
CG5	CD1	ILE- 84	3.75	0	Hydrophobic	false
C9	CD1	ILE- 84	3.54	0	Hydrophobic	false
C59	CD1	ILE- 84	3.36	0	Hydrophobic	false