scPDB - 1nyt entry

Protein Data Bank Entry:

PDB ID : 1nyt

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2003-02-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Shikimate dehydrogenase (NADP(+))
ID:	AROE_ECOLI
AC:	P15770
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:	12.104
Number of residues:	54
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.273	1272.375

% Hydrophobic	% Polar
48.01	51.99
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	62.03 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
49.8427	23.0067	21.1776

Binding mode :

What is Poseview ?

2D View
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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
C2D	CG1	VAL- 62	4.38	0	Hydrophobic	false
C5N	CE	LYS- 65	4.11	0	Hydrophobic	false
O3B	N	ALA- 127	3.03	166.48	H-Bond (Protein Donor)	false
O2A	N	GLY- 129	2.95	176.87	H-Bond (Protein Donor)	false
O2N	N	ALA- 130	2.84	168.32	H-Bond (Protein Donor)	false
C5D	CB	ALA- 130	4.1	0	Hydrophobic	false
C5N	CB	ALA- 130	3.79	0	Hydrophobic	false
O3B	OD1	ASN- 149	2.65	133.6	H-Bond (Ligand Donor)	false
O1X	ND2	ASN- 149	2.8	175.96	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 150	3.87	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 150	3.82	0	Ionic (Protein Cationic)	false
O2X	NE	ARG- 150	3.04	176.78	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 150	2.91	168.34	H-Bond (Protein Donor)	false
DuAr	CZ	ARG- 150	3.66	164.14	Pi/Cation	false
O2X	OG1	THR- 151	2.67	166.01	H-Bond (Protein Donor)	false
O2X	N	THR- 151	3.18	126.98	H-Bond (Protein Donor)	false
O1X	NH1	ARG- 154	2.95	157.38	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 154	3.96	0	Ionic (Protein Cationic)	false
C1B	CB	THR- 188	3.6	0	Hydrophobic	false
C5B	CB	SER- 189	4.44	0	Hydrophobic	false
C3D	CB	SER- 189	3.74	0	Hydrophobic	false
O4B	N	SER- 189	3.14	157.48	H-Bond (Protein Donor)	false
C3N	CB	MET- 213	4.36	0	Hydrophobic	false
C5N	SD	MET- 213	4.44	0	Hydrophobic	false
N7N	O	MET- 213	2.79	167.96	H-Bond (Ligand Donor)	false
N7N	O	GLY- 237	3.02	151.13	H-Bond (Ligand Donor)	false
C3N	SD	MET- 240	3.9	0	Hydrophobic	false
C4N	CE	MET- 240	3.43	0	Hydrophobic	false
O2N	O	HOH- 1432	2.73	179.97	H-Bond (Protein Donor)	false
N3A	O	HOH- 1448	3	179.95	H-Bond (Protein Donor)	false