scPDB - 4gte entry

Protein Data Bank Entry:

PDB ID : 4gte

Resolution :1.890 Å

Experimental Method : X-ray

Deposition Date : 2012-08-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Flavin-dependent thymidylate synthase
ID:	THYX_THEMA
AC:	Q9WYT0
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	2.1.1.148

Chains:

Chain Name:	Percentage of Residues within binding site
A	21 %
D	79 %

Ligand binding site composition:

B-Factor:	41.902
Number of residues:	14
Including
Standard Amino Acids:	13
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.211	901.125

% Hydrophobic	% Polar
35.58	64.42
According to VolSite

Ligand :

HET Code:	MEF
Formula:	C20H21N7O6
Molecular weight:	455.424 g/mol
DrugBank ID:	DB12676
Buried Surface Area:	52.34 %
Polar Surface area:	195.35 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	4
Rings:	4
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
47.5879	51.8047	129.441

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
N1	NH1	ARG- 174	2.72	149.71	H-Bond (Protein Donor)	false
N1	NH2	ARG- 174	3.36	126.35	H-Bond (Protein Donor)	false
C9	CB	HIS- 178	4.11	0	Hydrophobic	false
CM	C6	FAD- 301	4.49	0	Hydrophobic	false
C6	C6	FAD- 301	3.75	0	Hydrophobic	false
C7	C8	FAD- 301	4.4	0	Hydrophobic	false
N1	O2'	FAD- 301	2.59	161.03	H-Bond (Protein Donor)	false