scPDB - 1jmh entry

Protein Data Bank Entry:

PDB ID : 1jmh

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 1997-09-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	5.650	5.650	5.650	0.000	5.650	1

List of CHEMBLId :

CHEMBL211312

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:	23.195
Number of residues:	20
Including
Standard Amino Acids:	20
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.858	961.875

% Hydrophobic	% Polar
36.84	63.16
According to VolSite

Ligand :

HET Code:	UMP
Formula:	C9H11N2O8P
Molecular weight:	306.166 g/mol
DrugBank ID:	DB03800
Buried Surface Area:	38.9 %
Polar Surface area:	161.1 Å2

Number of
H-Bond Acceptors:	8
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
15.5258	49.5481	-55.7467

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
C5'	CD1	LEU- 195	3.84	0	Hydrophobic	false
C5'	SG	CYS- 198	4.06	0	Hydrophobic	false
C2'	SG	CYS- 198	3.93	0	Hydrophobic	false
OP1	CZ	ARG- 218	3.37	0	Ionic (Protein Cationic)	false
OP2	NH2	ARG- 218	3.3	163	H-Bond (Protein Donor)	false
OP1	OG	SER- 219	3.38	142.13	H-Bond (Protein Donor)	false
C2'	CB	SER- 219	4.25	0	Hydrophobic	false
O2	N	ASP- 221	2.74	141.05	H-Bond (Protein Donor)	false
C1'	CB	ASP- 221	4.42	0	Hydrophobic	false
O3'	NE2	HIS- 259	2.83	169.03	H-Bond (Ligand Donor)	false
O3'	OH	TYR- 261	3.26	154.47	H-Bond (Protein Donor)	false