scPDB - 1e5q entry

Protein Data Bank Entry:

PDB ID : 1e5q

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2000-07-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Saccharopine dehydrogenase [NADP(+), L-glutamate-forming]
ID:	LYS9_MAGO7
AC:	Q9P4R4
Organism:	Magnaporthe oryzae
Reign:	Eukaryota
TaxID:	242507
EC Number:	1.5.1.10

Chains:

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

Ligand binding site composition:

B-Factor:	24.920
Number of residues:	49
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.943	779.625

% Hydrophobic	% Polar
48.92	51.08
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	74.38 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
37.9979	43.6141	68.7092

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
O3B	N	SER- 11	3	154.85	H-Bond (Protein Donor)	false
O1A	N	PHE- 13	3.05	159.77	H-Bond (Protein Donor)	false
O2N	N	VAL- 14	3.18	175.85	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 14	4.24	0	Hydrophobic	false
C5N	CG1	VAL- 14	3.89	0	Hydrophobic	false
C2B	CB	CYS- 33	4.26	0	Hydrophobic	false
O2X	NH2	ARG- 34	3.34	156.39	H-Bond (Protein Donor)	false
O3X	NE	ARG- 34	3.02	154.34	H-Bond (Protein Donor)	false
O3X	CZ	ARG- 34	3.85	0	Ionic (Protein Cationic)	false
O3X	N	THR- 35	3.26	138.71	H-Bond (Protein Donor)	false
N6A	OD2	ASP- 55	3.07	151.18	H-Bond (Ligand Donor)	false
N1A	N	VAL- 56	3.12	169.94	H-Bond (Protein Donor)	false
C5D	CB	LEU- 75	4.28	0	Hydrophobic	false
C4B	CG2	ILE- 76	4.4	0	Hydrophobic	false
C1B	CG2	ILE- 76	3.64	0	Hydrophobic	false
O3D	O	ILE- 76	2.76	157.72	H-Bond (Ligand Donor)	false
N7N	O	THR- 98	2.76	151.18	H-Bond (Ligand Donor)	false
O7N	N	LEU- 125	2.87	136.69	H-Bond (Protein Donor)	false
O7N	N	ASP- 126	2.72	171.88	H-Bond (Protein Donor)	false
N7N	O	PRO- 127	3.01	157.54	H-Bond (Ligand Donor)	false
C5N	CB	TRP- 174	3.67	0	Hydrophobic	false
O1N	N	SER- 175	2.67	165.88	H-Bond (Protein Donor)	false
C4N	SD	MET- 395	4.09	0	Hydrophobic	false
C4N	CG2	VAL- 399	3.31	0	Hydrophobic	false
O2D	O1	SHR- 501	2.68	152.47	H-Bond (Ligand Donor)	false
C3N	C3	SHR- 501	4.3	0	Hydrophobic	false
C4N	C7	SHR- 501	4.3	0	Hydrophobic	false
O5B	O	HOH- 2062	3.11	156.51	H-Bond (Protein Donor)	false