scPDB - 2yyu entry

Protein Data Bank Entry:

PDB ID : 2yyu

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2007-05-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Orotidine 5'-phosphate decarboxylase
ID:	PYRF_GEOKA
AC:	Q5L0U0
Organism:	Geobacillus kaustophilus
Reign:	Bacteria
TaxID:	235909
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	15 %
B	85 %

Ligand binding site composition:

B-Factor:	21.828
Number of residues:	27
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.796	877.500

% Hydrophobic	% Polar
41.92	58.08
According to VolSite

Ligand :

HET Code:	C5P
Formula:	C9H12N3O8P
Molecular weight:	321.181 g/mol
DrugBank ID:	DB03403
Buried Surface Area:	43.88 %
Polar Surface area:	190.61 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
-20.9845	32.0828	31.2481

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
C4'	CB	ALA- 10	4.13	0	Hydrophobic	false
O3'	OD2	ASP- 12	3.25	129.82	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 12	3.32	170.86	H-Bond (Ligand Donor)	false
O3'	NZ	LYS- 34	2.65	134.23	H-Bond (Protein Donor)	false
O2'	NZ	LYS- 34	3.46	136.83	H-Bond (Protein Donor)	false
C2'	CD1	ILE- 67	4.37	0	Hydrophobic	false
N3	OG1	THR- 124	2.95	143.56	H-Bond (Protein Donor)	false
C1'	CB	PRO- 183	3.73	0	Hydrophobic	false
O3P	NH1	ARG- 186	2.93	133.26	H-Bond (Protein Donor)	false
O2P	NH2	ARG- 186	3.47	129.1	H-Bond (Protein Donor)	false
O3P	CZ	ARG- 186	3.69	0	Ionic (Protein Cationic)	false
C4'	CG1	VAL- 213	4.21	0	Hydrophobic	false
O1P	N	ARG- 216	2.63	148.61	H-Bond (Protein Donor)	false
O3P	O	HOH- 2341	3.36	128.47	H-Bond (Protein Donor)	false