scPDB - 5by6 entry

Protein Data Bank Entry:

PDB ID : 5by6

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2015-06-10

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:	Q9NDD3_TRISP
AC:	Q9NDD3
Organism:	Trichinella spiralis
Reign:	Eukaryota
TaxID:	6334
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	11 %
D	89 %

Ligand binding site composition:

B-Factor:	26.906
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.006	735.750

% Hydrophobic	% Polar
33.03	66.97
According to VolSite

Ligand :

HET Code:	UMP
Formula:	C9H11N2O8P
Molecular weight:	306.166 g/mol
DrugBank ID:	DB03800
Buried Surface Area:	62.52 %
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
18.3335	-2.805	-54.8558

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
O5'	NH2	ARG- 43	2.77	151.72	H-Bond (Protein Donor)	false
OP3	NE	ARG- 43	2.74	172.28	H-Bond (Protein Donor)	false
OP3	NH2	ARG- 43	3.35	131.39	H-Bond (Protein Donor)	false
OP3	CZ	ARG- 43	3.48	0	Ionic (Protein Cationic)	false
O5'	NH2	ARG- 169	3.41	149.25	H-Bond (Protein Donor)	false
OP1	NE	ARG- 169	3.07	157.97	H-Bond (Protein Donor)	false
OP3	NE	ARG- 169	3.42	133.65	H-Bond (Protein Donor)	false
OP3	NH2	ARG- 169	2.92	147.18	H-Bond (Protein Donor)	false
OP1	CZ	ARG- 169	3.9	0	Ionic (Protein Cationic)	false
OP3	CZ	ARG- 169	3.6	0	Ionic (Protein Cationic)	false
OP2	NE	ARG- 170	2.88	153.1	H-Bond (Protein Donor)	false
OP2	NH2	ARG- 170	3.03	141.46	H-Bond (Protein Donor)	false
OP2	CZ	ARG- 170	3.38	0	Ionic (Protein Cationic)	false
C5'	SG	CYS- 189	4.33	0	Hydrophobic	false
C2'	SG	CYS- 189	4.11	0	Hydrophobic	false
OP1	CZ	ARG- 209	3.86	0	Ionic (Protein Cationic)	false
OP2	CZ	ARG- 209	3.57	0	Ionic (Protein Cationic)	false
OP1	NH1	ARG- 209	2.89	154.31	H-Bond (Protein Donor)	false
OP2	NH2	ARG- 209	2.98	153.17	H-Bond (Protein Donor)	false
OP2	NH1	ARG- 209	3.3	136.27	H-Bond (Protein Donor)	false
C2'	CB	SER- 210	4.24	0	Hydrophobic	false
OP1	OG	SER- 210	2.63	162.48	H-Bond (Protein Donor)	false
O2	N	ASP- 212	2.86	165.26	H-Bond (Protein Donor)	false
C1'	CB	ASP- 212	3.93	0	Hydrophobic	false
N3	OD1	ASN- 220	2.9	169.39	H-Bond (Ligand Donor)	false
O4	ND2	ASN- 220	2.96	152.06	H-Bond (Protein Donor)	false
O3'	NE2	HIS- 250	2.76	165.26	H-Bond (Protein Donor)	false
O3'	OH	TYR- 252	2.75	163.43	H-Bond (Protein Donor)	false