scPDB - 3rl3 entry

Protein Data Bank Entry:

PDB ID : 3rl3

Resolution :1.420 Å

Experimental Method : X-ray

Deposition Date : 2011-04-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Metallophosphoesterase MPPED2
ID:	MPPD2_RAT
AC:	B1WBP0
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	3.1

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	17.736
Number of residues:	32
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	3
Water Molecules:	0
Cofactors:
Metals:	MN MN MN

Cavity properties

Ligandability	Volume (Å3)
0.381	475.875

% Hydrophobic	% Polar
56.74	43.26
According to VolSite

Ligand :

HET Code:	5GP
Formula:	C10H12N5O8P
Molecular weight:	361.205 g/mol
DrugBank ID:	-
Buried Surface Area:	67.46 %
Polar Surface area:	217.22 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
-24.8121	7.88367	3.62504

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
O1P	ND2	ASN- 117	2.88	145.03	H-Bond (Protein Donor)	false
O3P	NE2	HIS- 118	2.66	169.64	H-Bond (Protein Donor)	false
C1'	CE2	PHE- 183	4.22	0	Hydrophobic	false
DuAr	DuAr	PHE- 183	3.78	0	Aromatic Face/Face	false
O2'	NZ	LYS- 225	2.72	157.97	H-Bond (Protein Donor)	false
C2'	CD1	ILE- 253	4.09	0	Hydrophobic	false
O3'	N	HIS- 254	2.85	153.31	H-Bond (Protein Donor)	false
O3'	OE1	GLU- 255	2.59	157.78	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 255	2.61	152.1	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 255	3	138.41	H-Bond (Ligand Donor)	false
C5'	CZ	PHE- 277	4.1	0	Hydrophobic	false
O2P	MN	MN- 444	2.1	0	Metal Acceptor	false
O1P	MN	MN- 555	2.09	0	Metal Acceptor	false
O3P	MN	MN- 776	2.09	0	Metal Acceptor	false