scPDB - 1n1e entry

Protein Data Bank Entry:

PDB ID : 1n1e

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2002-10-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glycerol-3-phosphate dehydrogenase [NAD(+)], glycosomal
ID:	GPDA_LEIME
AC:	P90551
Organism:	Leishmania mexicana
Reign:	Eukaryota
TaxID:	5665
EC Number:	1.1.1.8

Chains:

Chain Name:	Percentage of Residues within binding site
A	2 %
B	98 %

Ligand binding site composition:

B-Factor:	18.497
Number of residues:	56
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.150	1127.250

% Hydrophobic	% Polar
51.80	48.20
According to VolSite

Ligand :

HET Code:	NDE
Formula:	C24H29N7O20P3
Molecular weight:	828.443 g/mol
DrugBank ID:	-
Buried Surface Area:	68.59 %
Polar Surface area:	463.07 Å2

Number of
H-Bond Acceptors:	24
H-Bond Donors:	7
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
24.6037	23.0224	20.7805

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	SER- 23	3.33	136.77	H-Bond (Protein Donor)	false
O3B	OG	SER- 23	2.76	152.32	H-Bond (Ligand Donor)	false
O2A	N	ALA- 25	2.86	175.95	H-Bond (Protein Donor)	false
C4N	CD2	PHE- 26	3.76	0	Hydrophobic	false
C1D	CD1	PHE- 26	4.18	0	Hydrophobic	false
O2N	N	PHE- 26	3.02	160.03	H-Bond (Protein Donor)	false
C5B	CE2	PHE- 63	3.97	0	Hydrophobic	false
C2B	CZ	PHE- 63	3.58	0	Hydrophobic	false
C3B	CE1	PHE- 63	3.81	0	Hydrophobic	false
C5D	CG1	VAL- 92	3.99	0	Hydrophobic	false
C5D	CG	PRO- 94	4.23	0	Hydrophobic	false
C4B	CG	PRO- 94	3.78	0	Hydrophobic	false
C1D	CG	LYS- 125	4.49	0	Hydrophobic	false
O3D	N	LYS- 125	3.11	170.74	H-Bond (Protein Donor)	false
O2	NZ	LYS- 125	2.88	173.83	H-Bond (Protein Donor)	false
O31	N	SER- 155	3.29	142.95	H-Bond (Protein Donor)	false
O31	OG	SER- 155	3.18	170.75	H-Bond (Protein Donor)	false
C1	CE2	PHE- 156	4.06	0	Hydrophobic	false
C3	CD2	PHE- 156	4.44	0	Hydrophobic	false
O7N	N	ALA- 157	2.87	148.04	H-Bond (Protein Donor)	false
O2	NZ	LYS- 210	2.67	159.53	H-Bond (Protein Donor)	false
O1N	NH2	ARG- 274	2.73	140.25	H-Bond (Protein Donor)	false
O1N	NH1	ARG- 274	2.98	130.84	H-Bond (Protein Donor)	false
O1P	NH2	ARG- 274	3.18	155.84	H-Bond (Protein Donor)	false
O3P	N	ARG- 274	2.99	159.14	H-Bond (Protein Donor)	false
O3P	NE	ARG- 274	2.78	165.53	H-Bond (Protein Donor)	false
O1N	CZ	ARG- 274	3.25	0	Ionic (Protein Cationic)	false
O1P	CZ	ARG- 274	3.96	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 274	3.6	0	Ionic (Protein Cationic)	false
O2P	N	ASN- 275	3.43	162.67	H-Bond (Protein Donor)	false
O2P	ND2	ASN- 275	2.87	164.24	H-Bond (Protein Donor)	false
O1A	N	VAL- 298	2.69	170.45	H-Bond (Protein Donor)	false
C5B	CG2	VAL- 298	3.9	0	Hydrophobic	false
O3D	OE1	GLU- 300	2.7	167.34	H-Bond (Ligand Donor)	false
C3D	CG	GLU- 300	3.86	0	Hydrophobic	false
O2N	O	HOH- 417	2.63	165.86	H-Bond (Protein Donor)	false
O1P	O	HOH- 473	2.58	179.97	H-Bond (Protein Donor)	false
O2B	O	HOH- 560	2.87	179.95	H-Bond (Protein Donor)	false