scPDB - 3phi entry

Protein Data Bank Entry:

PDB ID : 3phi

Resolution :2.040 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
B	100 %

Ligand binding site composition:

B-Factor:	35.259
Number of residues:	49
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.169	600.750

% Hydrophobic	% Polar
49.44	50.56
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	61.61 %
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
17.1639	-11.7908	16.0485

Binding mode :

What is Poseview ?

2D View
3D View

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
C3D	CD1	LEU- 66	4.08	0	Hydrophobic	false
O1N	NZ	LYS- 69	3.69	0	Ionic (Protein Cationic)	false
O3B	N	ALA- 126	2.87	171.27	H-Bond (Protein Donor)	false
O2A	N	GLY- 128	3.12	144.44	H-Bond (Protein Donor)	false
O2N	N	SER- 129	2.76	167.71	H-Bond (Protein Donor)	false
O5D	OG	SER- 129	3.13	167.8	H-Bond (Protein Donor)	false
O4D	OG	SER- 129	3.45	121.5	H-Bond (Protein Donor)	false
C5D	CB	SER- 129	4.2	0	Hydrophobic	false
C6N	CB	SER- 129	3.77	0	Hydrophobic	false
O3B	ND2	ASN- 148	3.42	160.6	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 149	3.84	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 149	3.98	0	Ionic (Protein Cationic)	false
O2X	NE	ARG- 149	3.14	170.76	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 149	3.04	155.98	H-Bond (Protein Donor)	false
DuAr	CZ	ARG- 149	3.69	159.75	Pi/Cation	false
C1B	CB	THR- 180	3.86	0	Hydrophobic	false
C5B	CB	SER- 181	4.08	0	Hydrophobic	false
O4B	N	SER- 181	3.13	140.78	H-Bond (Protein Donor)	false
C3D	CD1	LEU- 184	4.23	0	Hydrophobic	false
N6A	OE2	GLU- 187	3.28	136.74	H-Bond (Ligand Donor)	false
C1D	CB	LEU- 208	3.41	0	Hydrophobic	false
C6N	CD1	LEU- 208	3.78	0	Hydrophobic	false
N7N	O	GLY- 230	2.8	158.44	H-Bond (Ligand Donor)	false
O2N	O	HOH- 279	2.63	171.61	H-Bond (Protein Donor)	false