scPDB - 1ecb entry

Protein Data Bank Entry:

PDB ID : 1ecb

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 1997-07-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Amidophosphoribosyltransferase
ID:	PUR1_ECOLI
AC:	P0AG16
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	34.270
Number of residues:	27
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.053	283.500

% Hydrophobic	% Polar
42.86	57.14
According to VolSite

Ligand :

HET Code:	5GP
Formula:	C10H12N5O8P
Molecular weight:	361.205 g/mol
DrugBank ID:	-
Buried Surface Area:	52.75 %
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
22.0172	7.759	23.7293

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
C2'	CE1	TYR- 258	3.64	0	Hydrophobic	false
O3'	OD1	ASP- 367	2.72	156.44	H-Bond (Ligand Donor)	false
O3P	N	VAL- 370	3.22	148.38	H-Bond (Protein Donor)	false
C5'	CG2	VAL- 370	4.07	0	Hydrophobic	false
O2P	N	ARG- 371	2.82	163.45	H-Bond (Protein Donor)	false
O3P	N	ARG- 371	3.28	120.08	H-Bond (Protein Donor)	false
O3P	N	GLY- 372	2.66	151.86	H-Bond (Protein Donor)	false
O1P	OG1	THR- 374	2.78	168.12	H-Bond (Protein Donor)	false
O1P	N	THR- 374	3.25	168.85	H-Bond (Protein Donor)	false
O5'	OG1	THR- 374	3.12	120.83	H-Bond (Protein Donor)	false
C4'	CG2	THR- 374	4.49	0	Hydrophobic	false
O3'	MG	MG- 507	1.82	0	Metal Acceptor	false
O2'	MG	MG- 507	1.95	0	Metal Acceptor	false