scPDB - 1pkf entry

Protein Data Bank Entry:

PDB ID : 1pkf

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2003-06-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Epothilone C/D epoxidase
ID:	C167_SORCE
AC:	Q9KIZ4
Organism:	Sorangium cellulosum
Reign:	Bacteria
TaxID:	56
EC Number:	1.14

Chains:

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

Ligand binding site composition:

B-Factor:	41.200
Number of residues:	44
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.519	1346.625

% Hydrophobic	% Polar
59.65	40.35
According to VolSite

Ligand :

HET Code:	EPD
Formula:	C27H41NO5S
Molecular weight:	491.683 g/mol
DrugBank ID:	DB01873
Buried Surface Area:	68.94 %
Polar Surface area:	124.96 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
4.71588	40.0261	15.3999

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
C27	CG	MET- 90	4.09	0	Hydrophobic	false
S1	CB	LEU- 95	4.21	0	Hydrophobic	false
S1	CB	PHE- 96	4.22	0	Hydrophobic	false
C27	CD1	PHE- 96	4.49	0	Hydrophobic	false
C91	CE1	PHE- 96	3.82	0	Hydrophobic	false
DuAr	DuAr	PHE- 96	3.95	0	Aromatic Face/Face	false
O14	O	ALA- 180	2.97	170.41	H-Bond (Ligand Donor)	false
C15	CB	ALA- 180	4.41	0	Hydrophobic	false
C21	CD1	LEU- 183	3.33	0	Hydrophobic	false
C27	CD1	LEU- 183	3.48	0	Hydrophobic	false
C30	CB	LEU- 183	4.11	0	Hydrophobic	false
C28	CG1	VAL- 188	4.1	0	Hydrophobic	false
C29	CG2	VAL- 188	4.39	0	Hydrophobic	false
S1	CB	ALA- 250	3.75	0	Hydrophobic	false
C2	CB	ALA- 254	3.79	0	Hydrophobic	false
C51	CG2	THR- 258	3.49	0	Hydrophobic	false
C51	CD2	LEU- 301	4.25	0	Hydrophobic	false
C8	CD2	LEU- 301	4.12	0	Hydrophobic	false
O10	O	GLY- 304	2.89	165.73	H-Bond (Ligand Donor)	false
C7	CB	THR- 305	4.12	0	Hydrophobic	false
C9	CB	THR- 305	3.83	0	Hydrophobic	false
C28	CG1	VAL- 306	4.12	0	Hydrophobic	false
C28	CE2	PHE- 327	4.31	0	Hydrophobic	false
C29	CG	PRO- 401	4.37	0	Hydrophobic	false
C10	CB	ALA- 402	4.2	0	Hydrophobic	false
C15	CB	ALA- 402	3.55	0	Hydrophobic	false
C29	CB	ALA- 402	4.18	0	Hydrophobic	false
C51	CE2	PHE- 403	4.09	0	Hydrophobic	false