scPDB - 4hcy entry

Protein Data Bank Entry:

PDB ID : 4hcy

Resolution :2.750 Å

Experimental Method : X-ray

Deposition Date : 2012-10-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Transketolase
ID:	D2V4Z5_NAEGR
AC:	D2V4Z5
Organism:	Naegleria gruberi
Reign:	Eukaryota
TaxID:	5762
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	4 %
B	96 %

Ligand binding site composition:

B-Factor:	68.932
Number of residues:	26
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.349	2244.375

% Hydrophobic	% Polar
38.35	61.65
According to VolSite

Ligand :

HET Code:	0YN
Formula:	C13H17N3OS
Molecular weight:	263.359 g/mol
DrugBank ID:	-
Buried Surface Area:	61.5 %
Polar Surface area:	100.27 Å2

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

Mass center Coordinates

X	Y	Z
47.3605	30.6588	9.41983

Binding mode :

What is Poseview ?

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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
C2A	CE2	PHE- 13	4.16	0	Hydrophobic	false
S1	CB	TYR- 15	4.37	0	Hydrophobic	false
C4A	CE1	TYR- 53	4.04	0	Hydrophobic	false
C5A	CE1	TYR- 53	3.98	0	Hydrophobic	false
N4'	OH	TYR- 53	3.36	126.42	H-Bond (Ligand Donor)	false
N4'	OD2	ASP- 68	3.15	141.17	H-Bond (Ligand Donor)	false
C2A	CB	TYR- 116	4.18	0	Hydrophobic	false
C2A	CB	CYS- 118	4.12	0	Hydrophobic	false
C5'	SG	CYS- 118	4.28	0	Hydrophobic	false
C4A	CD2	PHE- 158	3.96	0	Hydrophobic	false
C5A	CD1	PHE- 158	3.63	0	Hydrophobic	false
C35	CZ	TYR- 230	4.23	0	Hydrophobic	false
C2A	CG	GLU- 232	4.32	0	Hydrophobic	false
C35	CG	TYR- 260	3.84	0	Hydrophobic	false
C4A	CE1	TYR- 260	3.62	0	Hydrophobic	false
C5'	CB	TYR- 260	4.31	0	Hydrophobic	false
N3'	OD1	ASP- 262	3.34	127.89	H-Bond (Ligand Donor)	false
N3'	OD2	ASP- 262	2.88	155.66	H-Bond (Ligand Donor)	false
N4'	OD1	ASP- 262	2.64	166.1	H-Bond (Ligand Donor)	false
C2A	CG2	THR- 300	4.45	0	Hydrophobic	false