scPDB - 3c9s entry

Protein Data Bank Entry:

PDB ID : 3c9s

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2008-02-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thiamine-monophosphate kinase
ID:	THIL_AQUAE
AC:	O67883
Organism:	Aquifex aeolicus
Reign:	Bacteria
TaxID:	224324
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	72 %
B	28 %

Ligand binding site composition:

B-Factor:	38.634
Number of residues:	45
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	3
Water Molecules:	2
Cofactors:
Metals:	MG MG MG

Cavity properties

Ligandability	Volume (Å3)
0.643	1059.750

% Hydrophobic	% Polar
36.31	63.69
According to VolSite

Ligand :

HET Code:	ACP
Formula:	C11H14N5O12P3
Molecular weight:	501.176 g/mol
DrugBank ID:	DB03909
Buried Surface Area:	63.04 %
Polar Surface area:	310.64 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
15.5372	50.4747	129.425

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
C5'	CD1	ILE- 12	4.27	0	Hydrophobic	false
C4'	CG2	ILE- 12	4.44	0	Hydrophobic	false
C1'	CG2	ILE- 12	4.37	0	Hydrophobic	false
C1'	CG2	ILE- 24	4	0	Hydrophobic	false
O3'	N	GLY- 25	2.91	156.59	H-Bond (Protein Donor)	false
O3'	O	ASP- 26	2.67	139.73	H-Bond (Ligand Donor)	false
N6	OH	TYR- 101	2.88	138.88	H-Bond (Ligand Donor)	false
O2'	N	GLY- 118	2.95	161.9	H-Bond (Protein Donor)	false
N6	O	ASN- 119	3.28	129.72	H-Bond (Ligand Donor)	false
O1B	CZ	ARG- 142	3.94	0	Ionic (Protein Cationic)	false
O1G	OG	SER- 209	2.95	139.31	H-Bond (Protein Donor)	false
O2B	MG	MG- 901	2.45	0	Metal Acceptor	false
O1A	MG	MG- 901	2.44	0	Metal Acceptor	false
O2G	MG	MG- 903	2.7	0	Metal Acceptor	false
O3G	MG	MG- 903	2.65	0	Metal Acceptor	false
O2B	MG	MG- 903	2.7	0	Metal Acceptor	false