scPDB - 1kzj entry

Protein Data Bank Entry:

PDB ID : 1kzj

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2002-02-06

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_ECOLI
AC:	P0A884
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	2 %
C	95 %
D	2 %

Ligand binding site composition:

B-Factor:	16.549
Number of residues:	44
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:	UMP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.236	884.250

% Hydrophobic	% Polar
51.91	48.09
According to VolSite

Ligand :

HET Code:	CB3
Formula:	C24H21N5O6
Molecular weight:	475.453 g/mol
DrugBank ID:	DB03541
Buried Surface Area:	59.15 %
Polar Surface area:	180.08 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
62.0954	31.6441	25.209

Binding mode :

What is Poseview ?

2D View
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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
CP1	CD1	ILE- 79	3.73	0	Hydrophobic	false
C14	CB	ILE- 79	3.35	0	Hydrophobic	false
C15	CG2	ILE- 79	3.27	0	Hydrophobic	false
N3	OD2	ASP- 169	2.98	170.46	H-Bond (Ligand Donor)	false
CP3	CB	PHE- 176	3.62	0	Hydrophobic	false
CP2	CD2	PHE- 176	3.56	0	Hydrophobic	false
CB	CD	LYS- 259	3.84	0	Hydrophobic	false
OE2	NZ	LYS- 259	3.73	0	Ionic (Protein Cationic)	false
C12	CG2	VAL- 262	4.39	0	Hydrophobic	false
NA2	O	ALA- 263	2.9	128.6	H-Bond (Ligand Donor)	false
CP3	C5	UMP- 304	4.42	0	Hydrophobic	false
C6	C5	UMP- 304	3.58	0	Hydrophobic	false