scPDB - 3kjm entry

Protein Data Bank Entry:

PDB ID : 3kjm

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2009-11-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cytokinin dehydrogenase 1
ID:	CKX1_MAIZE
AC:	Q9T0N8
Organism:	Zea mays
Reign:	Eukaryota
TaxID:	4577
EC Number:	1.5.99.12

Chains:

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

Ligand binding site composition:

B-Factor:	22.150
Number of residues:	28
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	1
Water Molecules:	6
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.339	779.625

% Hydrophobic	% Polar
50.22	49.78
According to VolSite

Ligand :

HET Code:	245
Formula:	C12H10ClN3O
Molecular weight:	247.680 g/mol
DrugBank ID:	-
Buried Surface Area:	66.64 %
Polar Surface area:	54.02 Å2

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

Mass center Coordinates

X	Y	Z
36.933	-19.3012	3.19241

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
CL7	CD1	LEU- 107	4.03	0	Hydrophobic	false
N2	OD2	ASP- 169	3.36	135.91	H-Bond (Ligand Donor)	false
N9	OD2	ASP- 169	2.88	156.76	H-Bond (Ligand Donor)	false
C11	CB	ASP- 169	3.87	0	Hydrophobic	false
C4	CG1	ILE- 184	4.46	0	Hydrophobic	false
C12	CG2	VAL- 378	3.58	0	Hydrophobic	false
C14	CG1	VAL- 378	3.64	0	Hydrophobic	false
C14	CD2	LEU- 388	4.08	0	Hydrophobic	false
CL7	CE3	TRP- 397	3.76	0	Hydrophobic	false
C13	CG	PRO- 427	4.08	0	Hydrophobic	false
C11	CD1	ILE- 429	3.53	0	Hydrophobic	false
C4	CB	SER- 456	4.49	0	Hydrophobic	false
C8	CD2	LEU- 458	4.16	0	Hydrophobic	false
C11	CD1	LEU- 458	4.36	0	Hydrophobic	false
C15	CD1	LEU- 458	3.53	0	Hydrophobic	false
CL7	CB	ALA- 492	4.25	0	Hydrophobic	false
CL7	C1'	FAD- 600	3.37	0	Hydrophobic	false