scPDB - 2ji6 entry

Protein Data Bank Entry:

PDB ID : 2ji6

Resolution :2.060 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	68 %
B	32 %

Ligand binding site composition:

B-Factor:	31.482
Number of residues:	55
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	2
Water Molecules:	7
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.355	2210.625

% Hydrophobic	% Polar
41.07	58.93
According to VolSite

Ligand :

HET Code:	TPW
Formula:	C13H16N3O7P2S
Molecular weight:	420.295 g/mol
DrugBank ID:	-
Buried Surface Area:	82.5 %
Polar Surface area:	221.44 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
73.5188	-5.90458	0.552308

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
C4A	CG1	VAL- 31	4.07	0	Hydrophobic	false
C35	CG1	VAL- 79	4.18	0	Hydrophobic	false
C5'	CG2	VAL- 79	3.82	0	Hydrophobic	false
C2A	CB	PRO- 82	3.88	0	Hydrophobic	false
S1	CB	ALA- 401	4.01	0	Hydrophobic	false
C5B	CB	ALA- 401	3.89	0	Hydrophobic	false
O11	N	ALA- 401	3.32	174.89	H-Bond (Protein Donor)	false
O22	N	ASN- 402	2.92	154.39	H-Bond (Protein Donor)	false
O22	ND2	ASN- 402	2.83	164.35	H-Bond (Protein Donor)	false
O21	N	ALA- 403	3.07	138.96	H-Bond (Protein Donor)	false
N4'	O	GLY- 426	2.73	158.59	H-Bond (Ligand Donor)	false
S1	CE	MET- 428	3.73	0	Hydrophobic	false
C4A	CG	MET- 428	4.36	0	Hydrophobic	false
C5A	CG	MET- 428	4.45	0	Hydrophobic	false
C5'	CG	MET- 428	4.07	0	Hydrophobic	false
N3'	N	MET- 428	3.39	170.05	H-Bond (Protein Donor)	false
O13	N	SER- 453	2.94	156.46	H-Bond (Protein Donor)	false
C5A	CB	SER- 453	3.59	0	Hydrophobic	false
O12	N	ALA- 454	2.9	155.85	H-Bond (Protein Donor)	false
C2A	CE2	PHE- 457	3.96	0	Hydrophobic	false
C4A	CZ	PHE- 457	4.09	0	Hydrophobic	false
O23	ND2	ASN- 479	3.17	134.85	H-Bond (Protein Donor)	false
C4A	CD1	ILE- 482	4.33	0	Hydrophobic	false
C5B	CG2	ILE- 482	3.67	0	Hydrophobic	false
C5B	CE1	TYR- 483	3.94	0	Hydrophobic	false
O23	N	TYR- 483	3.26	127.2	H-Bond (Protein Donor)	false
O13	MG	MG- 1567	2.22	0	Metal Acceptor	false
O23	MG	MG- 1567	2.1	0	Metal Acceptor	false
O21	O	HOH- 2374	2.89	131.61	H-Bond (Protein Donor)	false