scPDB - 1i33 entry

Protein Data Bank Entry:

PDB ID : 1i33

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2001-02-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glyceraldehyde-3-phosphate dehydrogenase, glycosomal
ID:	G3PG_LEIME
AC:	Q27890
Organism:	Leishmania mexicana
Reign:	Eukaryota
TaxID:	5665
EC Number:	1.2.1.12

Chains:

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

Ligand binding site composition:

B-Factor:	50.216
Number of residues:	27
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.325	256.500

% Hydrophobic	% Polar
60.53	39.47
According to VolSite

Ligand :

HET Code:	TND
Formula:	C29H32N6O6
Molecular weight:	560.601 g/mol
DrugBank ID:	DB04477
Buried Surface Area:	45.2 %
Polar Surface area:	152.87 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	6
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
51.8479	46.3792	29.8607

Binding mode :

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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
O3'	OD2	ASP- 38	3.02	159.47	H-Bond (Ligand Donor)	false
N2'	OD1	ASP- 38	3.19	153.14	H-Bond (Ligand Donor)	false
C6B	CG	MET- 39	3.61	0	Hydrophobic	false
C9	SD	MET- 39	3.95	0	Hydrophobic	false
C8	SD	MET- 39	3.32	0	Hydrophobic	false
C1B	CB	MET- 39	3.73	0	Hydrophobic	false
C2M	CB	SER- 40	3.95	0	Hydrophobic	false
C4B	CB	SER- 40	3.92	0	Hydrophobic	false
C2M	CD2	TYR- 45	4.43	0	Hydrophobic	false
C2M	CE1	PHE- 46	3.84	0	Hydrophobic	false
C8	CB	ALA- 90	4.09	0	Hydrophobic	false
N6A	O	GLN- 91	3.13	151.85	H-Bond (Ligand Donor)	false
C4	CD	ARG- 92	4.14	0	Hydrophobic	false
C5	CG	ARG- 92	3.29	0	Hydrophobic	false
C2	CD1	LEU- 113	3.51	0	Hydrophobic	false
C2M	CG2	VAL- 206	4.02	0	Hydrophobic	false
C4B	CG1	VAL- 206	3.7	0	Hydrophobic	false
C1M	CD1	LEU- 208	3.65	0	Hydrophobic	false
C3B	CD1	LEU- 208	3.49	0	Hydrophobic	false