scPDB - 2aaz entry

Protein Data Bank Entry:

PDB ID : 2aaz

Resolution :2.080 Å

Experimental Method : X-ray

Deposition Date : 2005-07-14

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_CRYNJ
AC:	P0CS12
Organism:	Cryptococcus neoformans var. neoformans serotype D
Reign:	Eukaryota
TaxID:	214684
EC Number:	2.1.1.45

Chains:

Chain Name:	Percentage of Residues within binding site
C	5 %
E	2 %
F	93 %

Ligand binding site composition:

B-Factor:	24.232
Number of residues:	50
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	1
Water Molecules:	8
Cofactors:	UMP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.357	2220.750

% Hydrophobic	% Polar
44.22	55.78
According to VolSite

Ligand :

HET Code:	CB3
Formula:	C24H21N5O6
Molecular weight:	475.453 g/mol
DrugBank ID:	DB03541
Buried Surface Area:	69.15 %
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
84.7023	37.7282	85.0314

Binding mode :

What is Poseview ?

2D View
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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
OE2	NH1	ARG- 70	3.01	147.56	H-Bond (Protein Donor)	false
CG	CG2	ILE- 100	4.36	0	Hydrophobic	false
CP1	CD1	ILE- 100	3.79	0	Hydrophobic	false
C13	CB	ILE- 100	3.35	0	Hydrophobic	false
C15	CG2	ILE- 100	4	0	Hydrophobic	false
C9	CZ2	TRP- 101	3.57	0	Hydrophobic	false
C8	CD2	LEU- 184	3.7	0	Hydrophobic	false
N3	OD1	ASP- 219	2.63	172.1	H-Bond (Ligand Donor)	false
C11	CB	LEU- 222	4.45	0	Hydrophobic	false
C15	CB	PHE- 226	4.26	0	Hydrophobic	false
CP1	CD2	PHE- 226	4.09	0	Hydrophobic	false
CP3	CB	PHE- 226	3.56	0	Hydrophobic	false
C4A	SD	MET- 315	4.1	0	Hydrophobic	false
C8	SD	MET- 315	3.56	0	Hydrophobic	false
C12	SD	MET- 315	3.88	0	Hydrophobic	false
NA2	O	SER- 316	2.93	140.4	H-Bond (Ligand Donor)	false
C6	C5	UMP- 600	3.77	0	Hydrophobic	false
NA2	O	HOH- 604	3.18	127.18	H-Bond (Ligand Donor)	false
N1	O	HOH- 1317	3.04	145.15	H-Bond (Protein Donor)	false
O1	O	HOH- 1377	2.75	179.96	H-Bond (Protein Donor)	false
O2	O	HOH- 1516	2.66	169.68	H-Bond (Protein Donor)	false