scPDB - 4isk entry

Protein Data Bank Entry:

PDB ID : 4isk

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2013-01-16

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
B	82 %
D	2 %
G	16 %

Ligand binding site composition:

B-Factor:	31.019
Number of residues:	58
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	1
Water Molecules:	7
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.351	2160.000

% Hydrophobic	% Polar
42.50	57.50
According to VolSite

Ligand :

HET Code:	1JY
Formula:	C32H30N5O10
Molecular weight:	644.608 g/mol
DrugBank ID:	-
Buried Surface Area:	55.08 %
Polar Surface area:	243.52 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	4
Rings:	4
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
49.8253	25.827	-83.3263

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
CAU	CD1	ILE- 79	3.89	0	Hydrophobic	false
CAX	CG2	ILE- 79	4.24	0	Hydrophobic	false
CBQ	CB	ILE- 79	3.97	0	Hydrophobic	false
CAQ	CG2	ILE- 79	3.58	0	Hydrophobic	false
CBP	CG2	ILE- 79	3.72	0	Hydrophobic	false
CAV	CZ3	TRP- 80	4.1	0	Hydrophobic	false
CAM	CE2	TRP- 80	3.58	0	Hydrophobic	false
CAN	CH2	TRP- 83	3.26	0	Hydrophobic	false
CAV	CZ3	TRP- 83	3.47	0	Hydrophobic	false
CAV	CD2	LEU- 143	3.65	0	Hydrophobic	false
NBA	OD2	ASP- 169	2.73	169.11	H-Bond (Ligand Donor)	false
OAH	OD2	ASP- 169	2.88	172.52	H-Bond (Ligand Donor)	false
CAU	CD2	PHE- 176	4.3	0	Hydrophobic	false
CAS	CB	PHE- 176	4.35	0	Hydrophobic	false
CAX	CZ	PHE- 176	4.18	0	Hydrophobic	false
CAA	CB	PHE- 176	3.65	0	Hydrophobic	false
CAA	CB	ASN- 177	4.5	0	Hydrophobic	false
CAT	CE2	TYR- 209	3.53	0	Hydrophobic	false
CG	CG	PRO- 256	3.74	0	Hydrophobic	false
CAT	CG2	VAL- 262	3.71	0	Hydrophobic	false
CAN	CG2	VAL- 262	4.45	0	Hydrophobic	false
CAT	CB	ALA- 263	3.92	0	Hydrophobic	false
OAH	N	ALA- 263	2.81	155.18	H-Bond (Protein Donor)	false
OAE	O	HOH- 425	2.84	156.49	H-Bond (Protein Donor)	false
OAD	O	HOH- 449	2.73	179.95	H-Bond (Protein Donor)	false
NBB	O	HOH- 453	3.27	179.99	H-Bond (Protein Donor)	false