scPDB - 5dmh entry

Protein Data Bank Entry:

PDB ID : 5dmh

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2015-09-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3-oxo-tetronate kinase
ID:	Q0KBC8_CUPNH
AC:	Q0KBC8
Organism:	Cupriavidus necator
Reign:	Bacteria
TaxID:	381666
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	19.274
Number of residues:	51
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.867	499.500

% Hydrophobic	% Polar
44.59	55.41
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	73.61 %
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
27.5653	73.1487	117.152

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
O3B	NE2	HIS- 155	2.58	173.98	H-Bond (Protein Donor)	false
C4'	CG	PRO- 156	4.23	0	Hydrophobic	false
C4'	CD2	LEU- 157	3.76	0	Hydrophobic	false
O2B	OG	SER- 272	2.57	165.42	H-Bond (Protein Donor)	false
N6	O	ALA- 324	3.27	162.56	H-Bond (Ligand Donor)	false
O2'	O	GLY- 344	2.9	136.85	H-Bond (Ligand Donor)	false
C2'	CG1	VAL- 347	4.35	0	Hydrophobic	false
C3'	CG	GLU- 348	4.24	0	Hydrophobic	false
O3'	OE2	GLU- 348	2.72	157.55	H-Bond (Ligand Donor)	false
O1B	N	GLY- 371	2.9	160.82	H-Bond (Protein Donor)	false
O2A	N	GLU- 372	2.81	165.24	H-Bond (Protein Donor)	false
O1A	N	THR- 373	3.1	148.25	H-Bond (Protein Donor)	false
O1A	OG1	THR- 373	2.78	163.6	H-Bond (Protein Donor)	false
O1B	N	GLY- 414	2.84	137.3	H-Bond (Protein Donor)	false
N3	O	HOH- 803	2.95	156.34	H-Bond (Protein Donor)	false