scPDB - 3ty3 entry

Protein Data Bank Entry:

PDB ID : 3ty3

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2011-09-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Homoisocitrate dehydrogenase
ID:	LYS12_SCHPO
AC:	O14104
Organism:	Schizosaccharomyces pombe
Reign:	Eukaryota
TaxID:	284812
EC Number:	1.1.1.87

Chains:

Chain Name:	Percentage of Residues within binding site
A	95 %
B	5 %

Ligand binding site composition:

B-Factor:	18.073
Number of residues:	24
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.089	1437.750

% Hydrophobic	% Polar
38.26	61.74
According to VolSite

Ligand :

HET Code:	GGG
Formula:	C6H11N3O4
Molecular weight:	189.169 g/mol
DrugBank ID:	-
Buried Surface Area:	49.5 %
Polar Surface area:	125.97 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	0
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
-8.87469	-2.66438	11.1184

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
N1	O	GLY- 77	2.92	130.1	H-Bond (Ligand Donor)	false
O1	N	VAL- 79	2.97	164.03	H-Bond (Protein Donor)	false
O2	OG	SER- 81	2.61	143.57	H-Bond (Protein Donor)	false
O3	NH1	ARG- 97	2.86	169.2	H-Bond (Protein Donor)	false
O3	CZ	ARG- 97	3.62	0	Ionic (Protein Cationic)	false
N1	OE1	GLU- 285	2.9	152.27	H-Bond (Ligand Donor)	false
N1	OE1	GLU- 285	2.9	0	Ionic (Ligand Cationic)	false
N1	O	PRO- 286	2.89	161.92	H-Bond (Ligand Donor)	false
N3	O	HOH- 454	2.8	134.53	H-Bond (Ligand Donor)	false