scPDB - 4brd entry

Protein Data Bank Entry:

PDB ID : 4brd

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2013-06-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ectonucleoside triphosphate diphosphohydrolase I
ID:	Q5ZUA2_LEGPH
AC:	Q5ZUA2
Organism:	Legionella pneumophila subsp. pneumophila
Reign:	Bacteria
TaxID:	272624
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.592
Number of residues:	43
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.285	769.500

% Hydrophobic	% Polar
30.26	69.74
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	58.11 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
61.3424	-2.74674	10.0155

Binding mode :

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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
O1G	N	SER- 52	2.95	151.26	H-Bond (Protein Donor)	false
N3B	OG	SER- 52	2.73	132.52	H-Bond (Ligand Donor)	false
O2B	OG1	THR- 53	2.58	175.01	H-Bond (Protein Donor)	false
O2B	N	THR- 53	2.94	153.43	H-Bond (Protein Donor)	false
C5'	CG2	THR- 53	3.88	0	Hydrophobic	false
O1B	CZ	ARG- 56	3.86	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 56	3.62	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 56	3.69	0	Ionic (Protein Cationic)	false
O1B	NH1	ARG- 56	2.98	157.13	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 56	2.89	166.02	H-Bond (Protein Donor)	false
O1G	OG1	THR- 118	2.88	154.11	H-Bond (Protein Donor)	false
O3A	N	GLY- 189	3.12	125.13	H-Bond (Protein Donor)	false
O3G	N	ALA- 190	2.77	162.29	H-Bond (Protein Donor)	false
O3G	N	SER- 191	3.07	161.62	H-Bond (Protein Donor)	false
C3'	CZ	TYR- 346	4.26	0	Hydrophobic	false
C2'	CE2	TYR- 346	3.57	0	Hydrophobic	false
O2G	MG	MG- 1394	2.01	0	Metal Acceptor	false
O1B	MG	MG- 1394	2.06	0	Metal Acceptor	false