scPDB - 4fqs entry

Protein Data Bank Entry:

PDB ID : 4fqs

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2012-06-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thymidylate synthase ThyA
ID:	TYSY_MYCTU
AC:	P9WFR9
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	2 %
B	98 %

Ligand binding site composition:

B-Factor:	17.450
Number of residues:	49
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	1
Water Molecules:	9
Cofactors:	UMP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.078	482.625

% Hydrophobic	% Polar
46.85	53.15
According to VolSite

Ligand :

HET Code:	LYA
Formula:	C20H19N5O6
Molecular weight:	425.395 g/mol
DrugBank ID:	DB00642
Buried Surface Area:	63.15 %
Polar Surface area:	192.63 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-12.784	-0.344645	5.55687

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
C25	CB	HIS- 51	4.47	0	Hydrophobic	false
C2	CD1	ILE- 79	3.99	0	Hydrophobic	false
C5	CB	ILE- 79	4.02	0	Hydrophobic	false
C7	CD1	ILE- 79	3.94	0	Hydrophobic	false
C25	CG2	ILE- 79	4.29	0	Hydrophobic	false
C6	CB	ILE- 79	3.8	0	Hydrophobic	false
C4	CG2	ILE- 79	4.16	0	Hydrophobic	false
C7	CE2	TRP- 80	4.04	0	Hydrophobic	false
C10	CH2	TRP- 80	3.45	0	Hydrophobic	false
C8	CZ2	TRP- 80	4.07	0	Hydrophobic	false
C10	CZ3	TRP- 83	3.72	0	Hydrophobic	false
C10	CD1	LEU- 143	4.19	0	Hydrophobic	false
N16	OD2	ASP- 169	2.75	151.11	H-Bond (Ligand Donor)	false
N19	OD2	ASP- 169	3.18	132.15	H-Bond (Ligand Donor)	false
C2	CB	PHE- 176	4.2	0	Hydrophobic	false
C25	CZ	PHE- 176	3.97	0	Hydrophobic	false
C2	CD1	PHE- 176	3.45	0	Hydrophobic	false
C5	CG2	VAL- 261	3.99	0	Hydrophobic	false
N19	O	ALA- 262	2.92	147.24	H-Bond (Ligand Donor)	false
N19	O	HOH- 406	3.23	123.26	H-Bond (Ligand Donor)	false
O30	O	HOH- 420	2.56	171.89	H-Bond (Protein Donor)	false
O31	O	HOH- 424	2.74	179.98	H-Bond (Protein Donor)	false
N18	O	HOH- 426	2.86	179.96	H-Bond (Protein Donor)	false
O30	O	HOH- 428	2.75	179.98	H-Bond (Protein Donor)	false
O28	O	HOH- 454	2.87	161.86	H-Bond (Protein Donor)	false