scPDB - 1e7y entry

Protein Data Bank Entry:

PDB ID : 1e7y

Resolution :2.480 Å

Experimental Method : X-ray

Deposition Date : 2000-09-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glucose-6-phosphate 1-dehydrogenase
ID:	G6PD_LEUME
AC:	P11411
Organism:	Leuconostoc mesenteroides
Reign:	Bacteria
TaxID:	1245
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	38.588
Number of residues:	25
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.295	256.500

% Hydrophobic	% Polar
59.21	40.79
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	52.42 %
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
95.066	-8.798	37.3802

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	THR- 14	3.49	147.93	H-Bond (Protein Donor)	false
O3X	OG1	THR- 14	3.04	143.36	H-Bond (Protein Donor)	false
O3B	OG1	THR- 14	2.7	156.59	H-Bond (Ligand Donor)	false
O2A	N	ASP- 16	2.81	149.59	H-Bond (Protein Donor)	false
C2B	CB	ALA- 45	4.2	0	Hydrophobic	false
O1X	NH2	ARG- 46	3.26	147.71	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 46	3.9	0	Ionic (Protein Cationic)	false
O2X	N	GLN- 47	2.74	160.54	H-Bond (Protein Donor)	false
O3X	NE2	GLN- 47	3.27	161.61	H-Bond (Protein Donor)	false
N6A	OD1	ASP- 85	2.99	129.75	H-Bond (Ligand Donor)	false
N1A	N	VAL- 86	3.2	161.46	H-Bond (Protein Donor)	false
C1B	CG1	VAL- 118	4.39	0	Hydrophobic	false