scPDB - 4ylh entry

Protein Data Bank Entry:

PDB ID : 4ylh

Resolution :2.580 Å

Experimental Method : X-ray

Deposition Date : 2015-03-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	(3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
ID:	DPGC_STRTO
AC:	Q8KLK7
Organism:	Streptomyces toyocaensis
Reign:	Bacteria
TaxID:	55952
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	2 %
K	98 %

Ligand binding site composition:

B-Factor:	35.878
Number of residues:	45
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.457	681.750

% Hydrophobic	% Polar
61.88	38.12
According to VolSite

Ligand :

HET Code:	YE1
Formula:	C29H39N8O19P3
Molecular weight:	896.583 g/mol
DrugBank ID:	-
Buried Surface Area:	58.31 %
Polar Surface area:	456.87 Å2

Number of
H-Bond Acceptors:	23
H-Bond Donors:	8
Rings:	4
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	21

Mass center Coordinates

X	Y	Z
66.3833	96.7917	-24.089

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
C1'	CB	ARG- 185	4.46	0	Hydrophobic	false
C4'	CG	LEU- 186	4.34	0	Hydrophobic	false
C5'	CD1	LEU- 186	3.74	0	Hydrophobic	false
OAL	OE1	GLU- 189	2.64	157.42	H-Bond (Ligand Donor)	false
OAL	OE2	GLU- 189	3.46	130.87	H-Bond (Ligand Donor)	false
O8A	NE2	HIS- 222	2.57	144.94	H-Bond (Protein Donor)	false
O5A	OH	TYR- 225	2.58	144.04	H-Bond (Protein Donor)	false
N4P	O	ALA- 233	2.66	157.94	H-Bond (Ligand Donor)	false
N6A	O	ILE- 235	2.99	141.16	H-Bond (Ligand Donor)	false
OAD	N	ILE- 235	2.57	161.63	H-Bond (Protein Donor)	false
CAC	CG2	ILE- 235	3.66	0	Hydrophobic	false
CAE	CB	ILE- 235	3.51	0	Hydrophobic	false
N1A	N	LEU- 237	3.06	166.6	H-Bond (Protein Donor)	false
O7A	NZ	LYS- 238	3.43	0	Ionic (Protein Cationic)	false
O9A	NZ	LYS- 238	3.04	0	Ionic (Protein Cationic)	false
O9A	NZ	LYS- 238	3.04	148.23	H-Bond (Protein Donor)	false
CAH	CD2	LEU- 251	3.94	0	Hydrophobic	false
CAI	CD	ARG- 254	4.09	0	Hydrophobic	false
C13	CZ	PHE- 292	4	0	Hydrophobic	false
C13	CD1	ILE- 294	3.65	0	Hydrophobic	false
C6P	CG2	ILE- 294	3.98	0	Hydrophobic	false
OAD	N	GLY- 296	3.03	155.81	H-Bond (Protein Donor)	false
CAC	CG1	ILE- 324	4.17	0	Hydrophobic	false
CAG	CD1	ILE- 324	3.58	0	Hydrophobic	false
OAK	O	ILE- 325	2.89	168.93	H-Bond (Ligand Donor)	false
OAK	N	GLY- 327	2.78	121.29	H-Bond (Protein Donor)	false
C2'	CE2	PHE- 432	4.46	0	Hydrophobic	false