scPDB - 4zdb entry

Protein Data Bank Entry:

PDB ID : 4zdb

Resolution :2.140 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
A	4 %
B	96 %

Ligand binding site composition:

B-Factor:	52.966
Number of residues:	23
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.747	735.750

% Hydrophobic	% Polar
45.41	54.59
According to VolSite

Ligand :

HET Code:	CAA
Formula:	C25H36N7O18P3S
Molecular weight:	847.576 g/mol
DrugBank ID:	DB03059
Buried Surface Area:	37.03 %
Polar Surface area:	446.75 Å2

Number of
H-Bond Acceptors:	23
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	22

Mass center Coordinates

X	Y	Z
110.773	131.792	247.709

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	4.02	0	Hydrophobic	false
CCP	CD1	LEU- 30	4.41	0	Hydrophobic	false
CEP	CE2	PHE- 65	3.59	0	Hydrophobic	false
CCP	CZ	PHE- 65	3.5	0	Hydrophobic	false
N7A	OG	SER- 68	2.75	154.52	H-Bond (Protein Donor)	false
N6A	O	ALA- 70	2.88	166.47	H-Bond (Ligand Donor)	false
N1A	N	PHE- 72	3.1	154.51	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 72	3.81	0	Aromatic Face/Face	false
N3A	NZ	LYS- 73	3.3	124.38	H-Bond (Protein Donor)	false
CEP	CD1	ILE- 124	3.25	0	Hydrophobic	false
C6P	CG2	ILE- 124	4.24	0	Hydrophobic	false
S1P	CB	PRO- 149	3.81	0	Hydrophobic	false
S1P	CB	ASN- 152	3.75	0	Hydrophobic	false