scPDB - 4zdc entry

Protein Data Bank Entry:

PDB ID : 4zdc

Resolution :2.130 Å

Experimental Method : X-ray

Deposition Date : 2015-04-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3,2-trans-enoyl-CoA isomerase
ID:	ECI1_YEAST
AC:	Q05871
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	5.3.3.8

Chains:

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

Ligand binding site composition:

B-Factor:	63.005
Number of residues:	20
Including
Standard Amino Acids:	20
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.642	344.250

% Hydrophobic	% Polar
52.94	47.06
According to VolSite

Ligand :

HET Code:	CO8
Formula:	C29H46N7O17P3S
Molecular weight:	889.699 g/mol
DrugBank ID:	DB02910
Buried Surface Area:	35.11 %
Polar Surface area:	429.68 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	26

Mass center Coordinates

X	Y	Z
225.645	249.633	248.006

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
C5B	CG	LEU- 30	4.12	0	Hydrophobic	false
CCP	CD1	LEU- 30	4.07	0	Hydrophobic	false
CEP	CE2	PHE- 65	3.38	0	Hydrophobic	false
CCP	CZ	PHE- 65	4.38	0	Hydrophobic	false
N6A	OG	SER- 68	3.2	122.82	H-Bond (Ligand Donor)	false
N6A	O	SER- 68	3.49	137.02	H-Bond (Ligand Donor)	false
N7A	OG	SER- 68	2.66	155.66	H-Bond (Protein Donor)	false
N6A	O	ALA- 70	2.96	166.11	H-Bond (Ligand Donor)	false
N1A	N	PHE- 72	3.14	157.76	H-Bond (Protein Donor)	false
N3A	NZ	LYS- 73	2.89	169.45	H-Bond (Protein Donor)	false
CEP	CD1	ILE- 124	3.41	0	Hydrophobic	false