scPDB - 2ji8 entry

Protein Data Bank Entry:

PDB ID : 2ji8

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2007-02-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Oxalyl-CoA decarboxylase
ID:	OXC_OXAFO
AC:	P40149
Organism:	Oxalobacter formigenes
Reign:	Bacteria
TaxID:	847
EC Number:	4.1.1.8

Chains:

Chain Name:	Percentage of Residues within binding site
A	8 %
B	92 %

Ligand binding site composition:

B-Factor:	34.212
Number of residues:	54
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:	TPP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.720	1755.000

% Hydrophobic	% Polar
45.58	54.42
According to VolSite

Ligand :

HET Code:	FYN
Formula:	C22H32N7O17P3S
Molecular weight:	791.512 g/mol
DrugBank ID:	-
Buried Surface Area:	59.68 %
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:	20

Mass center Coordinates

X	Y	Z
39.7252	18.31	-0.6955

Binding mode :

What is Poseview ?

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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
CP8	CE	MET- 247	4.27	0	Hydrophobic	false
C2'	CB	ARG- 266	4.25	0	Hydrophobic	false
O2'	N	ARG- 266	3.1	162.99	H-Bond (Protein Donor)	false
O33	N	ALA- 267	2.69	170.64	H-Bond (Protein Donor)	false
CP9	CZ3	TRP- 285	4.49	0	Hydrophobic	false
CP4	CH2	TRP- 285	4.18	0	Hydrophobic	false
CP8	CD2	LEU- 286	3.79	0	Hydrophobic	false
CP1	CB	ALA- 401	4.37	0	Hydrophobic	false
CP4	CD2	LEU- 404	3.61	0	Hydrophobic	false
O11	NH2	ARG- 408	3.18	144	H-Bond (Protein Donor)	false
O11	NE	ARG- 408	3.01	157.53	H-Bond (Protein Donor)	false
O11	CZ	ARG- 408	3.54	0	Ionic (Protein Cationic)	false
C1'	CG	MET- 409	4.29	0	Hydrophobic	false
CP1	CE	MET- 428	4.23	0	Hydrophobic	false
OM2	OG	SER- 553	3.04	138.72	H-Bond (Protein Donor)	false
C5'	CD	ARG- 555	4.2	0	Hydrophobic	false
O21	NH1	ARG- 555	3.39	154.41	H-Bond (Protein Donor)	false
O22	NE	ARG- 555	3.19	139.63	H-Bond (Protein Donor)	false
CP9	CG2	ILE- 556	4.11	0	Hydrophobic	false
CP4	CD1	ILE- 556	3.88	0	Hydrophobic	false
S	CD1	ILE- 556	3.44	0	Hydrophobic	false
CP1	S1	TPP- 1563	3.48	0	Hydrophobic	false
NP1	O	HOH- 2231	3.23	166.34	H-Bond (Ligand Donor)	false