scPDB - 2kce entry

Protein Data Bank Entry:

PDB ID : 2kce

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 1997-06-09

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
A	3 %
B	97 %

Ligand binding site composition:

B-Factor:	24.390
Number of residues:	42
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:	UMP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.190	509.625

% Hydrophobic	% Polar
52.98	47.02
According to VolSite

Ligand :

HET Code:	D16
Formula:	C21H20N4O6S
Molecular weight:	456.472 g/mol
DrugBank ID:	DB00293
Buried Surface Area:	65.29 %
Polar Surface area:	182.3 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
46.8798	40.4897	22.4107

Binding mode :

What is Poseview ?

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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
O2	NE2	HIS- 51	3.49	139.22	H-Bond (Protein Donor)	false
OE1	OG	SER- 54	3.43	150.56	H-Bond (Protein Donor)	false
OE2	OG	SER- 54	3.41	145.27	H-Bond (Protein Donor)	false
S13	CB	ILE- 79	3.87	0	Hydrophobic	false
CG	CG2	ILE- 79	4.07	0	Hydrophobic	false
C9	CZ2	TRP- 80	3.67	0	Hydrophobic	false
C8	CH2	TRP- 83	3.42	0	Hydrophobic	false
C8	CD2	LEU- 143	3.76	0	Hydrophobic	false
N3	OD2	ASP- 169	2.82	161.91	H-Bond (Ligand Donor)	false
CP1	CD1	PHE- 176	3.94	0	Hydrophobic	false
CM2	CE2	TYR- 209	3.61	0	Hydrophobic	false
CM2	CG1	VAL- 262	4.23	0	Hydrophobic	false
C4A	CG1	VAL- 262	4.47	0	Hydrophobic	false
CM2	CB	ALA- 263	3.89	0	Hydrophobic	false
CM2	C4'	UMP- 567	3.61	0	Hydrophobic	false
C6	C5	UMP- 567	3.82	0	Hydrophobic	false
N1	O	HOH- 588	2.8	156.33	H-Bond (Protein Donor)	false
O2	O	HOH- 613	2.99	149.92	H-Bond (Protein Donor)	false
O1	O	HOH- 749	2.74	151.81	H-Bond (Protein Donor)	false
O2	O	HOH- 757	3.07	157.85	H-Bond (Protein Donor)	false