scPDB - 2cft entry

Protein Data Bank Entry:

PDB ID : 2cft

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2006-02-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pyridoxal phosphate phosphatase
ID:	PLPP_HUMAN
AC:	Q96GD0
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	23.227
Number of residues:	36
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
0.392	496.125

% Hydrophobic	% Polar
40.14	59.86
According to VolSite

Ligand :

HET Code:	PLP
Formula:	C8H8NO6P
Molecular weight:	245.126 g/mol
DrugBank ID:	DB00114
Buried Surface Area:	64.47 %
Polar Surface area:	132.42 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	1
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
23.4532	19.3188	17.8903

Binding mode :

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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
C5A	CB	ASP- 27	3.62	0	Hydrophobic	false
O2P	N	ASP- 27	2.98	178.05	H-Bond (Protein Donor)	false
O4P	OG	SER- 58	3.47	120.63	H-Bond (Protein Donor)	false
O2P	OG	SER- 58	2.63	169.53	H-Bond (Protein Donor)	false
O3P	N	ASN- 59	2.84	170.89	H-Bond (Protein Donor)	false
C5	CB	ASN- 60	3.94	0	Hydrophobic	false
C2A	CD1	TYR- 150	3.27	0	Hydrophobic	false
DuAr	DuAr	HIS- 182	3.51	0	Aromatic Face/Face	false
C4	CB	HIS- 182	4.45	0	Hydrophobic	false
O3P	NZ	LYS- 213	2.9	167.67	H-Bond (Protein Donor)	false
O3P	NZ	LYS- 213	2.9	0	Ionic (Protein Cationic)	false
O1P	CA	CA- 1297	2.26	0	Metal Acceptor	false
O4A	O	HOH- 2067	3.31	155.78	H-Bond (Protein Donor)	false
N1	O	HOH- 2159	3.01	151.87	H-Bond (Protein Donor)	false
O1P	O	HOH- 2193	3.08	167.94	H-Bond (Protein Donor)	false