scPDB - 1yon entry

Protein Data Bank Entry:

PDB ID : 1yon

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2005-01-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	4.220	4.220	4.220	0.000	4.220	1

List of CHEMBLId :

CHEMBL1161862

Binding Site :

Uniprot Annotation

Name:	2-dehydropantoate 2-reductase
ID:	PANE_ECOLI
AC:	P0A9J4
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	1.1.1.169

Chains:

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

Ligand binding site composition:

B-Factor:	36.139
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.941	1657.125

% Hydrophobic	% Polar
39.71	60.29
According to VolSite

Ligand :

HET Code:	A2R
Formula:	C15H20N5O17P3
Molecular weight:	635.264 g/mol
DrugBank ID:	-
Buried Surface Area:	53.03 %
Polar Surface area:	378.8 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	4
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
15.9782	0.8241	10.0862

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
O12	N	ALA- 10	2.9	163.22	H-Bond (Protein Donor)	false
C1'	CD2	LEU- 11	4.37	0	Hydrophobic	false
O1	N	LEU- 11	2.89	167.61	H-Bond (Protein Donor)	false
C5'	CG	LYS- 72	3.96	0	Hydrophobic	false
C3'	CG	LYS- 72	4.13	0	Hydrophobic	false
O12'	NZ	LYS- 72	3.43	120.72	H-Bond (Protein Donor)	false
O11'	NZ	LYS- 72	2.77	150.73	H-Bond (Protein Donor)	false
C1'	CB	HIS- 97	4.46	0	Hydrophobic	false
C4'	CB	HIS- 97	4.11	0	Hydrophobic	false
OP3	ND2	ASN- 98	3.17	130.43	H-Bond (Protein Donor)	false
O2'	ND2	ASN- 98	2.91	153.31	H-Bond (Protein Donor)	false
O3'	N	ASN- 98	3	169.28	H-Bond (Protein Donor)	false
C2'	CB	ASN- 98	4.4	0	Hydrophobic	false
N1	N	THR- 118	3.16	151.88	H-Bond (Protein Donor)	false
N6	O	THR- 118	2.56	141.03	H-Bond (Ligand Donor)	false
C14'	CD	ARG- 124	4.01	0	Hydrophobic	false
C13'	CB	ARG- 124	4.35	0	Hydrophobic	false
OP3	OG	SER- 244	2.67	167.89	H-Bond (Protein Donor)	false
C11'	CD	ARG- 253	4.13	0	Hydrophobic	false
O3'	OE2	GLU- 256	2.61	173.32	H-Bond (Ligand Donor)	false
O1	O	HOH- 568	2.85	159.92	H-Bond (Protein Donor)	false