scPDB - 5iot entry

Protein Data Bank Entry:

PDB ID : 5iot

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2016-03-08

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
C	48 %
D	52 %

Ligand binding site composition:

B-Factor:	26.752
Number of residues:	22
Including
Standard Amino Acids:	20
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.209	381.375

% Hydrophobic	% Polar
45.13	54.87
According to VolSite

Ligand :

HET Code:	UMP
Formula:	C9H11N2O8P
Molecular weight:	306.166 g/mol
DrugBank ID:	DB03800
Buried Surface Area:	77.37 %
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
0.2979	19.2565	-44.5341

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
C2'	CG	GLN- 75	4.14	0	Hydrophobic	false
OP3	NE2	GLN- 75	2.88	168.27	H-Bond (Protein Donor)	false
O3'	NH1	ARG- 78	3.02	155.39	H-Bond (Protein Donor)	false
C2'	CG	ARG- 78	3.83	0	Hydrophobic	false
C4'	CB	GLU- 86	3.9	0	Hydrophobic	false
C5'	CB	SER- 88	4.4	0	Hydrophobic	false
OP2	OG	SER- 88	2.57	176.02	H-Bond (Protein Donor)	false
OP1	N	GLY- 89	2.79	161.43	H-Bond (Protein Donor)	false
O4	NH1	ARG- 90	2.84	142.27	H-Bond (Protein Donor)	false
OP1	NH1	ARG- 147	2.8	152.62	H-Bond (Protein Donor)	false
OP3	NH1	ARG- 147	3.25	129.77	H-Bond (Protein Donor)	false
OP3	NH2	ARG- 147	2.64	162.69	H-Bond (Protein Donor)	false
OP1	CZ	ARG- 147	3.75	0	Ionic (Protein Cationic)	false
OP3	CZ	ARG- 147	3.38	0	Ionic (Protein Cationic)	false
C1'	C1'	FAD- 301	4.23	0	Hydrophobic	false