scPDB - 1nja entry

Protein Data Bank Entry:

PDB ID : 1nja

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 1996-01-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thymidylate synthase
ID:	TYSY_LACCA
AC:	P00469
Organism:	Lactobacillus casei
Reign:	Bacteria
TaxID:	1582
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	26.122
Number of residues:	24
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.109	1117.125

% Hydrophobic	% Polar
45.02	54.98
According to VolSite

Ligand :

HET Code:	DCM
Formula:	C9H12N3O7P
Molecular weight:	305.181 g/mol
DrugBank ID:	-
Buried Surface Area:	52.23 %
Polar Surface area:	170.38 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
15.4785	47.51	-54.3344

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
C5'	CD1	LEU- 195	3.79	0	Hydrophobic	false
C5'	SG	CYS- 198	4.43	0	Hydrophobic	false
C2'	SG	CYS- 198	3.79	0	Hydrophobic	false
O2P	NH1	ARG- 218	3.09	148.36	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 218	3.11	155.93	H-Bond (Protein Donor)	false
O2P	CZ	ARG- 218	3.72	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 218	3.87	0	Ionic (Protein Cationic)	false
O2P	OG	SER- 219	3.03	151.26	H-Bond (Protein Donor)	false
C2'	CB	SER- 219	4.01	0	Hydrophobic	false
O2	N	ASP- 221	2.78	149.85	H-Bond (Protein Donor)	false
C1'	CB	ASP- 221	4.23	0	Hydrophobic	false
O3'	NE2	HIS- 259	2.66	163.64	H-Bond (Ligand Donor)	false
O3'	OH	TYR- 261	2.7	146.03	H-Bond (Protein Donor)	false