scPDB - 1ebu entry

Protein Data Bank Entry:

PDB ID : 1ebu

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2000-01-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Homoserine dehydrogenase
ID:	DHOM_YEAST
AC:	P31116
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	1.1.1.3

Chains:

Chain Name:	Percentage of Residues within binding site
D	100 %

Ligand binding site composition:

B-Factor:	22.323
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.217	610.875

% Hydrophobic	% Polar
39.23	60.77
According to VolSite

Ligand :

HET Code:	NDA
Formula:	C21H29N7O13P2
Molecular weight:	649.442 g/mol
DrugBank ID:	DB03797
Buried Surface Area:	55.53 %
Polar Surface area:	328.09 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	2
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
44.1183	21.9254	70.6721

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
O3B	N	ALA- 13	2.68	154.02	H-Bond (Protein Donor)	false
O2A	N	VAL- 15	3.06	151.67	H-Bond (Protein Donor)	false
O1N	N	VAL- 16	2.99	172.55	H-Bond (Protein Donor)	false
O2N	N	VAL- 16	3.29	122.79	H-Bond (Protein Donor)	false
C5D	CB	VAL- 16	4.03	0	Hydrophobic	false
C3N	CG2	VAL- 16	3.88	0	Hydrophobic	false
O2N	N	GLY- 17	3.31	161.89	H-Bond (Protein Donor)	false
C4B	CG2	THR- 93	4.5	0	Hydrophobic	false
C1B	CG2	THR- 93	3.96	0	Hydrophobic	false
C3D	CB	SER- 94	3.78	0	Hydrophobic	false
C4D	CG	PRO- 115	3.9	0	Hydrophobic	false
C4N	CB	ALA- 339	3.92	0	Hydrophobic	false
C3N	CB	THR- 344	4.38	0	Hydrophobic	false
C5N	CG2	THR- 344	4.15	0	Hydrophobic	false
N7N	O1	HSE- 1301	3.59	0	Ionic (Ligand Cationic)	false
C4N	C4	HSE- 1301	3.69	0	Hydrophobic	false