scPDB - 1lol entry

Protein Data Bank Entry:

PDB ID : 1lol

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2002-05-06

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_METTH
AC:	O26232
Organism:	Methanothermobacter thermautotrophicus
Reign:	Archaea
TaxID:	187420
EC Number:	4.1.1.23

Chains:

Chain Name:	Percentage of Residues within binding site
A	19 %
B	81 %

Ligand binding site composition:

B-Factor:	25.805
Number of residues:	28
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.133	664.875

% Hydrophobic	% Polar
37.56	62.44
According to VolSite

Ligand :

HET Code:	XMP
Formula:	C10H11N4O9P
Molecular weight:	362.190 g/mol
DrugBank ID:	DB02309
Buried Surface Area:	49.68 %
Polar Surface area:	207.94 Å2

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

Mass center Coordinates

X	Y	Z
-19.5882	62.2837	52.5314

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
C3'	CB	ALA- 1018	4.19	0	Hydrophobic	false
C5'	CB	ALA- 1018	3.75	0	Hydrophobic	false
O3'	OD2	ASP- 1020	3.38	127.91	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 1020	2.51	165.92	H-Bond (Ligand Donor)	false
O2'	NZ	LYS- 1042	2.9	156.97	H-Bond (Protein Donor)	false
O3'	NZ	LYS- 1042	3	123.74	H-Bond (Protein Donor)	false
C1'	CG	PRO- 1180	4.42	0	Hydrophobic	false
C4'	CB	PRO- 1180	4.35	0	Hydrophobic	false
C4'	CG2	ILE- 1200	4.12	0	Hydrophobic	false
O3P	N	GLY- 1202	2.89	155.69	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 1203	3.59	0	Ionic (Protein Cationic)	false
O2P	N	ARG- 1203	2.84	170.9	H-Bond (Protein Donor)	false
O2P	NH1	ARG- 1203	3.46	139	H-Bond (Protein Donor)	false
O3P	O	HOH- 3159	3.03	145.84	H-Bond (Protein Donor)	false