scPDB - 3t2v entry

Protein Data Bank Entry:

PDB ID : 3t2v

Resolution :2.510 Å

Experimental Method : X-ray

Deposition Date : 2011-07-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Peptidoglycan recognition protein 1
ID:	PGRP1_CAMDR
AC:	Q9GK12
Organism:	Camelus dromedarius
Reign:	Eukaryota
TaxID:	9838
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	35 %
B	53 %
D	12 %

Ligand binding site composition:

B-Factor:	59.781
Number of residues:	16
Including
Standard Amino Acids:	16
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.128	1144.125

% Hydrophobic	% Polar
34.22	65.78
According to VolSite

Ligand :

HET Code:	KKJ
Formula:	C15H29O3
Molecular weight:	257.389 g/mol
DrugBank ID:	-
Buried Surface Area:	36.44 %
Polar Surface area:	60.36 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	1
Rings:	0
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
-34.1414	-20.9741	-40.9012

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
C9	CB	ASP- 2	4.47	0	Hydrophobic	false
C10	CB	PRO- 3	4.33	0	Hydrophobic	false
C18	SG	CYS- 6	3.94	0	Hydrophobic	false
C18	CB	CYS- 6	4.42	0	Hydrophobic	false
C14	CB	CYS- 6	3.59	0	Hydrophobic	false
O5	NH2	ARG- 31	3.14	141.2	H-Bond (Protein Donor)	false
C12	CB	ALA- 129	4.18	0	Hydrophobic	false
C3	CD2	LEU- 134	4.45	0	Hydrophobic	false