scPDB - 1npd entry

Protein Data Bank Entry:

PDB ID : 1npd

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2003-01-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Quinate/shikimate dehydrogenase
ID:	YDIB_ECOLI
AC:	P0A6D5
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	40.800
Number of residues:	42
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.828	769.500

% Hydrophobic	% Polar
32.46	67.54
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	63.31 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-11.7017	-29.9731	-9.2742

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- 132	2.9	167.32	H-Bond (Protein Donor)	false
O2A	N	GLY- 134	3.07	153.34	H-Bond (Protein Donor)	false
O2N	N	ALA- 135	2.9	172.21	H-Bond (Protein Donor)	false
C5D	CB	ALA- 135	4.49	0	Hydrophobic	false
C5N	CB	ALA- 135	4.34	0	Hydrophobic	false
O3B	OD1	ASN- 155	2.75	140.87	H-Bond (Ligand Donor)	false
O2B	ND2	ASN- 155	3.26	124.68	H-Bond (Protein Donor)	false
DuAr	CZ	ARG- 156	3.99	150.11	Pi/Cation	false
O2B	OD2	ASP- 158	2.62	168.12	H-Bond (Ligand Donor)	false
C5B	CZ	PHE- 160	4.19	0	Hydrophobic	false
C3B	CG	PHE- 160	3.66	0	Hydrophobic	false
C2B	CD1	PHE- 160	3.96	0	Hydrophobic	false
C4B	CB	THR- 204	4.45	0	Hydrophobic	false
C1B	CB	THR- 204	3.66	0	Hydrophobic	false
C5B	CG	LYS- 205	4.03	0	Hydrophobic	false
C3D	CG	LYS- 205	4.48	0	Hydrophobic	false
O4B	N	LYS- 205	3.26	137.17	H-Bond (Protein Donor)	false
C3D	SD	MET- 208	4	0	Hydrophobic	false
N7N	O	CYS- 232	3.5	149.9	H-Bond (Ligand Donor)	false
C4D	CG2	VAL- 233	4.35	0	Hydrophobic	false
N7N	O	GLY- 255	3.13	137.44	H-Bond (Ligand Donor)	false
C3N	SD	MET- 258	4.27	0	Hydrophobic	false