scPDB - 1yjq entry

Protein Data Bank Entry:

PDB ID : 1yjq

Resolution :2.090 Å

Experimental Method : X-ray

Deposition Date : 2005-01-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	6.590	6.590	6.590	0.000	6.590	1

List of CHEMBLId :

CHEMBL295069

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:	25.005
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.443	644.625

% Hydrophobic	% Polar
36.65	63.35
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	54.33 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
19.9654	2.78554	7.7036

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
O2A	N	ALA- 10	3.14	168.66	H-Bond (Protein Donor)	false
O2N	N	LEU- 11	2.96	164.52	H-Bond (Protein Donor)	false
C3N	CD1	LEU- 11	4.24	0	Hydrophobic	false
O1X	CZ	ARG- 31	3.77	0	Ionic (Protein Cationic)	false
O2X	CZ	ARG- 31	3.57	0	Ionic (Protein Cationic)	false
O1X	NH2	ARG- 31	3.1	162.66	H-Bond (Protein Donor)	false
O2X	NE	ARG- 31	2.69	138.05	H-Bond (Protein Donor)	false
C4B	CD2	LEU- 71	4.45	0	Hydrophobic	false
C1B	CD2	LEU- 71	3.87	0	Hydrophobic	false
C5B	CG	LYS- 72	4.5	0	Hydrophobic	false
C5D	CG	LYS- 72	4.39	0	Hydrophobic	false
C3D	CD	LYS- 72	4.4	0	Hydrophobic	false
C4D	CB	HIS- 97	3.96	0	Hydrophobic	false
O3D	N	ASN- 98	3	163.93	H-Bond (Protein Donor)	false
C2D	CB	ASN- 98	4.24	0	Hydrophobic	false
C5N	CG2	THR- 118	3.6	0	Hydrophobic	false
O7N	N	ALA- 122	2.87	175.16	H-Bond (Protein Donor)	false
N7N	O	ALA- 122	2.99	147.3	H-Bond (Ligand Donor)	false
O3D	OE2	GLU- 256	2.66	159.69	H-Bond (Ligand Donor)	false
O2D	OE1	GLU- 256	3.06	162.52	H-Bond (Ligand Donor)	false
O2N	O	HOH- 715	2.81	179.95	H-Bond (Protein Donor)	false