scPDB - 3s1d entry

Protein Data Bank Entry:

PDB ID : 3s1d

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2011-05-15

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:	23.697
Number of residues:	39
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.542	904.500

% Hydrophobic	% Polar
58.96	41.04
According to VolSite

Ligand :

HET Code:	ZIR
Formula:	C15H21N5O4
Molecular weight:	335.358 g/mol
DrugBank ID:	DB11933
Buried Surface Area:	61.03 %
Polar Surface area:	125.55 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
-38.2259	-15.026	-3.6895

Binding mode :

What is Poseview ?

2D View
3D View

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
C15	CD1	ILE- 184	4.3	0	Hydrophobic	false
C2'	CG2	VAL- 378	4.05	0	Hydrophobic	false
O2'	OG	SER- 381	2.67	145.47	H-Bond (Protein Donor)	false
O3'	OG	SER- 381	3.05	170.71	H-Bond (Ligand Donor)	false
C14	CZ3	TRP- 397	3.48	0	Hydrophobic	false
C1'	CG	PRO- 427	4.19	0	Hydrophobic	false
C4'	CB	PRO- 427	4.31	0	Hydrophobic	false
C15	CB	SER- 456	4.11	0	Hydrophobic	false
C14	CD2	LEU- 458	3.94	0	Hydrophobic	false
C15	CE2	TYR- 491	4.46	0	Hydrophobic	false
C14	CD1	LEU- 492	3.81	0	Hydrophobic	false
C15	CD1	LEU- 492	4.39	0	Hydrophobic	false
C14	C9A	FAD- 535	4.07	0	Hydrophobic	false
N7	O	HOH- 927	3.38	179.98	H-Bond (Protein Donor)	false