scPDB - 1ef9 entry

Protein Data Bank Entry:

PDB ID : 1ef9

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2000-02-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methylmalonyl-CoA decarboxylase
ID:	SCPB_ECOLI
AC:	P52045
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	4.1.1.41

Chains:

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

Ligand binding site composition:

B-Factor:	40.293
Number of residues:	34
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.238	637.875

% Hydrophobic	% Polar
51.85	48.15
According to VolSite

Ligand :

HET Code:	2CP
Formula:	C25H37N7O18P3S
Molecular weight:	848.584 g/mol
DrugBank ID:	DB03117
Buried Surface Area:	41.12 %
Polar Surface area:	452.74 Å2

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

Mass center Coordinates

X	Y	Z
-6.44267	-30.2255	42.5281

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
CPB	CD1	LEU- 25	4.33	0	Hydrophobic	false
CP8	CD1	LEU- 25	4.24	0	Hydrophobic	false
CP8	CG1	VAL- 61	4.09	0	Hydrophobic	false
N6	O	ALA- 64	3.42	136.93	H-Bond (Ligand Donor)	false
NP1	O	ALA- 64	2.87	130.85	H-Bond (Ligand Donor)	false
CP8	CB	ALA- 64	3.38	0	Hydrophobic	false
N6	O	HIS- 66	2.64	155.08	H-Bond (Ligand Donor)	false
S	CB	HIS- 66	4.05	0	Hydrophobic	false
N1	N	ILE- 68	3.23	162.13	H-Bond (Protein Donor)	false
CP1	CD1	ILE- 68	4.5	0	Hydrophobic	false
S	CD2	LEU- 71	4.25	0	Hydrophobic	false
CP9	CZ2	TRP- 108	3.45	0	Hydrophobic	false
CP8	CE2	TRP- 108	4.3	0	Hydrophobic	false
CP4	CB	TRP- 108	3.87	0	Hydrophobic	false
OS4	N	GLY- 110	2.77	160.62	H-Bond (Protein Donor)	false
OP1	OG1	THR- 132	2.88	159.55	H-Bond (Protein Donor)	false
CS3	CB	PRO- 133	3.89	0	Hydrophobic	false
S	CD2	LEU- 136	4.34	0	Hydrophobic	false
CS1	CD1	LEU- 136	4.36	0	Hydrophobic	false
CS3	CE1	TYR- 140	3.77	0	Hydrophobic	false