scPDB - 1f28 entry

Protein Data Bank Entry:

PDB ID : 1f28

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2000-05-23

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_PNECA
AC:	P13100
Organism:	Pneumocystis carinii
Reign:	Eukaryota
TaxID:	4754
EC Number:	2.1.1.45

Chains:

Chain Name:	Percentage of Residues within binding site
C	98 %
D	2 %

Ligand binding site composition:

B-Factor:	38.250
Number of residues:	43
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:	UMP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.042	604.125

% Hydrophobic	% Polar
56.42	43.58
According to VolSite

Ligand :

HET Code:	F89
Formula:	C27H22N4O6
Molecular weight:	498.487 g/mol
DrugBank ID:	-
Buried Surface Area:	63.76 %
Polar Surface area:	154.06 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	2
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
1.69514	5.17592	68.6902

Binding mode :

What is Poseview ?

2D View
3D View

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
N12	OE1	GLU- 65	3.34	160.21	H-Bond (Ligand Donor)	false
C18	CB	GLU- 65	4.47	0	Hydrophobic	false
C17	CG2	ILE- 84	4.47	0	Hydrophobic	false
CG	CB	HIS- 85	4.25	0	Hydrophobic	false
C14	CG2	ILE- 86	3.54	0	Hydrophobic	false
CG	CG1	ILE- 86	3.93	0	Hydrophobic	false
C6A	CG2	ILE- 86	4.34	0	Hydrophobic	false
C16	CG1	ILE- 86	3.22	0	Hydrophobic	false
C5	CD1	LEU- 170	3.69	0	Hydrophobic	false
N2	OD1	ASP- 202	2.68	169.7	H-Bond (Ligand Donor)	false
C10	CD2	LEU- 205	4.33	0	Hydrophobic	false
C14	CD2	LEU- 205	4.28	0	Hydrophobic	false
C11	CB	PHE- 209	3.77	0	Hydrophobic	false
C13	CB	PHE- 209	3.82	0	Hydrophobic	false
DuAr	DuAr	PHE- 209	3.93	0	Aromatic Face/Face	false
C3M	CE2	TYR- 242	3.76	0	Hydrophobic	false
C3M	CG	MET- 295	4.23	0	Hydrophobic	false
C5	SD	MET- 295	4.47	0	Hydrophobic	false
C3M	CB	SER- 296	4.01	0	Hydrophobic	false
C3M	C4'	UMP- 303	4	0	Hydrophobic	false
C1A	C5	UMP- 303	4.4	0	Hydrophobic	false
C1B	C5	UMP- 303	3.94	0	Hydrophobic	false