scPDB - 1dna entry

Protein Data Bank Entry:

PDB ID : 1dna

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 1998-06-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thymidylate synthase
ID:	TYSY_ECOLI
AC:	P0A884
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	3 %
B	97 %

Ligand binding site composition:

B-Factor:	38.453
Number of residues:	40
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:	UMP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.313	654.750

% Hydrophobic	% Polar
53.61	46.39
According to VolSite

Ligand :

HET Code:	CB3
Formula:	C24H21N5O6
Molecular weight:	475.453 g/mol
DrugBank ID:	DB03541
Buried Surface Area:	61.06 %
Polar Surface area:	180.08 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
47.0321	40.4952	22.3369

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
OE1	OG	SER- 54	3.23	154.13	H-Bond (Protein Donor)	false
CP1	CD1	ILE- 79	4.41	0	Hydrophobic	false
C16	CG2	ILE- 79	3.73	0	Hydrophobic	false
C15	CB	ILE- 79	3.52	0	Hydrophobic	false
C9	CZ2	TRP- 80	3.96	0	Hydrophobic	false
C8	CH2	TRP- 83	3.44	0	Hydrophobic	false
C8	CD2	LEU- 143	3.7	0	Hydrophobic	false
N3	ND2	ASN- 169	2.94	168.08	H-Bond (Protein Donor)	false
C13	CB	PHE- 176	4.38	0	Hydrophobic	false
CP1	CD2	PHE- 176	4.12	0	Hydrophobic	false
CP3	CB	PHE- 176	3.72	0	Hydrophobic	false
C8A	C4'	UMP- 604	4.28	0	Hydrophobic	false
CP3	C5	UMP- 604	4.5	0	Hydrophobic	false
C6	C5	UMP- 604	3.77	0	Hydrophobic	false
N1	O	HOH- 853	2.85	172.35	H-Bond (Ligand Donor)	false
O1	O	HOH- 893	2.92	167.08	H-Bond (Protein Donor)	false