scPDB - 2ji7 entry

Protein Data Bank Entry:

PDB ID : 2ji7

Resolution :1.820 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	82 %
B	18 %

Ligand binding site composition:

B-Factor:	25.389
Number of residues:	85
Including
Standard Amino Acids:	79
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.879	1623.375

% Hydrophobic	% Polar
45.53	54.47
According to VolSite

Ligand :

HET Code:	OXT
Formula:	C34H48N11O24P5S2
Molecular weight:	1213.803 g/mol
DrugBank ID:	-
Buried Surface Area:	66.56 %
Polar Surface area:	658.15 Å2

Number of
H-Bond Acceptors:	32
H-Bond Donors:	7
Rings:	5
Aromatic rings:	4
Anionic atoms:	7
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	29

Mass center Coordinates

X	Y	Z
77.9873	-14.8678	-1.184

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
CM4	CG1	VAL- 31	4.24	0	Hydrophobic	false
N11	OE2	GLU- 56	2.59	152.1	H-Bond (Ligand Donor)	false
C51	CG2	VAL- 79	3.9	0	Hydrophobic	false
CM2	CB	PRO- 82	3.89	0	Hydrophobic	false
C33	CE	MET- 247	4.35	0	Hydrophobic	false
C2'	CB	ARG- 266	4.27	0	Hydrophobic	false
O2'	N	ARG- 266	3.09	153.94	H-Bond (Protein Donor)	false
O81	N	ALA- 267	2.94	165.86	H-Bond (Protein Donor)	false
C34	CZ3	TRP- 285	4.1	0	Hydrophobic	false
C64	CH2	TRP- 285	4.04	0	Hydrophobic	false
C34	CD2	LEU- 286	3.79	0	Hydrophobic	false
O2B	OH	TYR- 377	2.65	130.67	H-Bond (Protein Donor)	false
S16	CB	ALA- 401	4.01	0	Hydrophobic	false
C76	CB	ALA- 401	3.67	0	Hydrophobic	false
O3A	N	ALA- 401	3.21	177.28	H-Bond (Protein Donor)	false
O1B	N	ASN- 402	2.83	153.82	H-Bond (Protein Donor)	false
O1B	ND2	ASN- 402	2.76	158.7	H-Bond (Protein Donor)	false
O2B	N	ALA- 403	3.09	136.85	H-Bond (Protein Donor)	false
C64	CD2	LEU- 404	4.12	0	Hydrophobic	false
O13	CZ	ARG- 408	3.25	0	Ionic (Protein Cationic)	false
O13	NE	ARG- 408	2.97	139.57	H-Bond (Protein Donor)	false
O13	NH2	ARG- 408	2.68	153.31	H-Bond (Protein Donor)	false
C1'	CE	MET- 409	4.4	0	Hydrophobic	false
C5'	CE	MET- 409	3.65	0	Hydrophobic	false
N41	O	GLY- 426	2.77	156.72	H-Bond (Ligand Donor)	false
C25	CE	MET- 428	3.87	0	Hydrophobic	false
C51	CG	MET- 428	4.01	0	Hydrophobic	false
CM2	CB	MET- 428	4.44	0	Hydrophobic	false
CM4	CG	MET- 428	4.24	0	Hydrophobic	false
S16	SD	MET- 428	3.79	0	Hydrophobic	false
C66	SD	MET- 428	4.18	0	Hydrophobic	false
N31	N	MET- 428	3.38	167.27	H-Bond (Protein Donor)	false
O1A	N	SER- 453	3.02	156.77	H-Bond (Protein Donor)	false
C66	CB	SER- 453	3.73	0	Hydrophobic	false
O2A	N	ALA- 454	2.99	157.63	H-Bond (Protein Donor)	false
CM2	CE2	PHE- 457	3.73	0	Hydrophobic	false
CM4	CZ	PHE- 457	4.16	0	Hydrophobic	false
O3B	ND2	ASN- 479	3.16	139.35	H-Bond (Protein Donor)	false
C76	CG2	ILE- 482	3.96	0	Hydrophobic	false
C76	CE1	TYR- 483	3.99	0	Hydrophobic	false
O3B	N	TYR- 483	3.07	131.76	H-Bond (Protein Donor)	false
O71	NH2	ARG- 555	2.95	138.3	H-Bond (Protein Donor)	false
O43	NH2	ARG- 555	2.93	148.53	H-Bond (Protein Donor)	false
O53	NE	ARG- 555	2.89	133.59	H-Bond (Protein Donor)	false
O71	CZ	ARG- 555	3.97	0	Ionic (Protein Cationic)	false
O43	CZ	ARG- 555	3.79	0	Ionic (Protein Cationic)	false
O53	CZ	ARG- 555	3.69	0	Ionic (Protein Cationic)	false
C5'	CD	ARG- 555	4.06	0	Hydrophobic	false
C34	CG2	ILE- 556	4.25	0	Hydrophobic	false
C64	CD1	ILE- 556	3.87	0	Hydrophobic	false
S15	CD1	ILE- 556	3.76	0	Hydrophobic	false
O1A	MG	MG- 1567	2.14	0	Metal Acceptor	false
O3B	MG	MG- 1567	2.02	0	Metal Acceptor	false
O2B	O	HOH- 2479	2.86	135.02	H-Bond (Protein Donor)	false