scPDB - 2pyw entry

Protein Data Bank Entry:

PDB ID : 2pyw

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2007-05-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methylthioribose kinase
ID:	MTK_ARATH
AC:	Q9C6D2
Organism:	Arabidopsis thaliana
Reign:	Eukaryota
TaxID:	3702
EC Number:	2.7.1.100

Chains:

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

Ligand binding site composition:

B-Factor:	20.667
Number of residues:	34
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.996	469.125

% Hydrophobic	% Polar
60.43	39.57
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	72.36 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
19.4372	40.1261	20.7157

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
C1'	CG2	VAL- 42	4.46	0	Hydrophobic	false
O3'	OD1	ASP- 44	2.68	154.71	H-Bond (Ligand Donor)	false
O1B	N	LEU- 47	3.23	150.36	H-Bond (Protein Donor)	false
O1B	N	ASN- 48	2.91	148.35	H-Bond (Protein Donor)	false
O2B	ND2	ASN- 48	2.84	150.83	H-Bond (Protein Donor)	false
C5'	CG1	VAL- 50	4.02	0	Hydrophobic	false
C4'	CG2	VAL- 50	4.26	0	Hydrophobic	false
C1'	CG2	VAL- 50	3.94	0	Hydrophobic	false
O2B	NZ	LYS- 63	3.21	145.34	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 63	2.74	140.91	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 63	3.21	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 63	2.74	0	Ionic (Protein Cationic)	false
N6	O	ARG- 117	2.96	150.97	H-Bond (Ligand Donor)	false
N1	N	LEU- 119	2.88	163.83	H-Bond (Protein Donor)	false
C3'	CD1	ILE- 125	3.97	0	Hydrophobic	false
C2'	CG1	ILE- 125	4.19	0	Hydrophobic	false
C2'	SD	MET- 245	4.16	0	Hydrophobic	false
C3'	CD1	ILE- 254	4.1	0	Hydrophobic	false
O2B	MG	MG- 500	2.07	0	Metal Acceptor	false
O3B	MG	MG- 501	2.02	0	Metal Acceptor	false
O2A	MG	MG- 501	2.09	0	Metal Acceptor	false