scPDB - 3phj entry

Protein Data Bank Entry:

PDB ID : 3phj

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2010-11-04

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_HELPY
AC:	P56119
Organism:	Helicobacter pylori
Reign:	Bacteria
TaxID:	85962
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	22.694
Number of residues:	28
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.081	691.875

% Hydrophobic	% Polar
45.85	54.15
According to VolSite

Ligand :

HET Code:	DHK
Formula:	C7H9O5
Molecular weight:	173.143 g/mol
DrugBank ID:	-
Buried Surface Area:	70.77 %
Polar Surface area:	100.82 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	1
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
14.7238	-0.594667	42.8061

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
C6	CG2	VAL- 8	4.46	0	Hydrophobic	false
O1	OG	SER- 16	2.73	162.23	H-Bond (Protein Donor)	false
O1	OG	SER- 18	2.73	154.11	H-Bond (Protein Donor)	false
C5	CB	ASN- 63	4.24	0	Hydrophobic	false
C5	CB	THR- 65	4.46	0	Hydrophobic	false
C1	CB	THR- 65	3.85	0	Hydrophobic	false
O3	NZ	LYS- 69	2.87	166.72	H-Bond (Protein Donor)	false
O4	ND2	ASN- 90	3.1	163.36	H-Bond (Protein Donor)	false
O5	ND2	ASN- 90	3.33	121.89	H-Bond (Protein Donor)	false
O4	OD1	ASP- 105	2.92	169.58	H-Bond (Ligand Donor)	false
O2	OH	TYR- 210	2.54	159.32	H-Bond (Protein Donor)	false
C1	CD1	LEU- 234	4.35	0	Hydrophobic	false
C4	CG	GLN- 237	4.24	0	Hydrophobic	false
O5	OE1	GLN- 237	2.79	172.33	H-Bond (Ligand Donor)	false