scPDB - 3rt4 entry

Protein Data Bank Entry:

PDB ID : 3rt4

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2011-05-03

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	8 %
C	48 %
D	44 %

Ligand binding site composition:

B-Factor:	22.712
Number of residues:	50
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.984	1103.625

% Hydrophobic	% Polar
34.56	65.44
According to VolSite

Ligand :

HET Code:	LP5
Formula:	C34H64NO12P
Molecular weight:	709.845 g/mol
DrugBank ID:	-
Buried Surface Area:	64.75 %
Polar Surface area:	227.77 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	5
Rings:	1
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	30

Mass center Coordinates

X	Y	Z
-28.401	-28.0022	-20.8452

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
C16	CH2	TRP- 66	4.36	0	Hydrophobic	false
C26	CH2	TRP- 66	3.89	0	Hydrophobic	false
C3	CZ2	TRP- 66	4.2	0	Hydrophobic	false
C4	CE2	TRP- 66	4.4	0	Hydrophobic	false
C29	CE2	TRP- 66	3.97	0	Hydrophobic	false
C31	CE2	TRP- 66	4.36	0	Hydrophobic	false
O48	NZ	LYS- 90	2.64	151.53	H-Bond (Protein Donor)	false
O48	NZ	LYS- 90	2.64	0	Ionic (Protein Cationic)	false
C27	CB	ALA- 92	4.33	0	Hydrophobic	false
C5	CB	ALA- 92	4.37	0	Hydrophobic	false
C1	CG	PRO- 96	3.79	0	Hydrophobic	false
C3	CG	PRO- 96	4.23	0	Hydrophobic	false
O42	OG1	THR- 97	2.55	168.33	H-Bond (Protein Donor)	false
O42	N	THR- 97	3.22	123.81	H-Bond (Protein Donor)	false
C32	CG2	THR- 97	4.22	0	Hydrophobic	false
C30	CB	THR- 97	3.82	0	Hydrophobic	false
C36	CZ2	TRP- 98	3.93	0	Hydrophobic	false
C38	CZ2	TRP- 98	4.33	0	Hydrophobic	false
C40	CH2	TRP- 98	3.7	0	Hydrophobic	false
C34	CE2	TRP- 98	4.1	0	Hydrophobic	false
O46	ND2	ASN- 99	3.33	140.46	H-Bond (Protein Donor)	false
O1	ND2	ASN- 99	2.5	143.47	H-Bond (Protein Donor)	false
O7	ND2	ASN- 99	3.17	146.58	H-Bond (Protein Donor)	false
C41	CB	SER- 139	3.82	0	Hydrophobic	false
C33	CB	ASN- 140	4.25	0	Hydrophobic	false
C38	CD	LYS- 144	4.24	0	Hydrophobic	false
O43	O	VAL- 149	2.57	153.01	H-Bond (Ligand Donor)	false
C34	CB	VAL- 149	4.14	0	Hydrophobic	false
C36	CG1	VAL- 149	3.92	0	Hydrophobic	false
C19	CB	GLN- 150	3.74	0	Hydrophobic	false
C23	CB	GLN- 150	4.29	0	Hydrophobic	false
O3	NE2	GLN- 150	3.49	145.04	H-Bond (Protein Donor)	false
C22	CG	PRO- 151	4.43	0	Hydrophobic	false
C24	CG	PRO- 151	3.95	0	Hydrophobic	false
C18	CG	PRO- 151	3.65	0	Hydrophobic	false
C20	CB	THR- 152	4.16	0	Hydrophobic	false
C21	CB	THR- 152	4.32	0	Hydrophobic	false
O6	NE	ARG- 170	3.3	129.24	H-Bond (Protein Donor)	false
O43	O	HOH- 180	2.8	179.96	H-Bond (Protein Donor)	false