PDBe-KB Ligand Pages (PDBeChem)

Examples: STI GLC NAG HEM CLC_000191 PRD_000468

AMZ

AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE

Description

Synonyms

AICAR, AICA-ribonucleotide, acadesine 5'-monophosphate, 5-am...Show more

Formula

C9 H15 N4 O8 P

Standard InChI

InChI=1S/C9H15N4O8P/c10-7-4(8(11)16)12-2-13(7)9-6(15)5(14)3(21-9)1-20-22(17,18)19/h2-3,5-6,9,14-15H,1,10H2,(H2,11,16)(H2...Show more

Standard InChI Key

NOTGFIUVDGNKRI-UUOKFMHZSA-N

SMILES

c1nc(c(n1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)N)C(=O...Show more

Source OpenEye

First observed in

1m9n

Overall view, and highlighted
scaffolds and fragments
This image gallery displays several views of the ligand structure:
Basic Structural Representation: Shows the overall structure of the ligand.
Detailed Structural Representation: Highlights individual atoms within the ligand.
Murcko Scaffold: Presents the scaffold of the ligand highlighted in yellow.
Highlighted Fragments: Displays various ligand fragments, highlighted in yellow.

Displayed: 1 / 7

Atom labelled AMZ

Physicochemical properties

Molecular properties

Molecular weight

Total mass of the molecule in Daltons

338.1 Da

Labute accessible surface area

Accessible surface area according to the Labute's definition

144.7 Å ²

Heavy atoms

Number of non-hydrogen atoms

Heteroatoms

Number of non-oxygen and non-carbon atoms

Carbon SP3 value

Fraction of C atoms that are SP3 hybridized

0.6

Wildman-Crippen molar refractivity

Wildman-Crippen molar refractivity is a common descriptor accounting for molecular size and polarizability

68.0

Wildman-Crippen Log P

Octanol/Water partition coefficient predicted using Wildman-Crippen method

-3.1

Conformational properties

Rotatable bonds

Number of single bonds, not part of a ring bound to a nonterminal heavy atom

Ring properties

Aromatic rings

Number of aromatic rings

Rings

Number of rings

Aliphatic rings

Number of aliphatic rings

Heterocycles

Number or rings with at least two different elements

Saturated rings

Number of saturated rings

Aromatic heterocycles

Number of aromatic heterocyles

Saturated heterocycles

Number of saturated heterocyles

Aliphatic heterocycles

Number of aliphatic heterocycles

Spiro atoms

Atoms shared between rings that share exactly one atom

Bridgehead atoms

Number of atoms shared between rings that share at least two bonds

Surface properties

Topological surface area

203.4

Functional group properties

Hydrogen bond donors

Number of hydrogen bond donors

Hydrogen bond acceptors

Number of hydrogen bond acceptors

Amide bonds

Number of amide bonds

Stereochemical properties

Stereocenters

Number of atoms with four attachments different from each other

Bound structures

Found as a bound ligand in 13 distinct proteins and 23 PDB Structures. Group data by:

Proteins

Structures

1 to 10 of 14. Page 1 of 2

Protein name

Protein Overview

Total structures

Organism

EC number

Ligand function

Unmapped

Unannotated

Bifunctional purine biosynthesis protein ATIC

P31939

Homo sapiens (Human)

3.5.4.10, 2.1.2.3

Unannotated

5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase

Q57600

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

6.3.4.23

Unannotated

Bifunctional purine biosynthesis protein ATIC

P31335

Gallus gallus (Chicken)

3.5.4.10, 2.1.2.3

Unannotated

Adenylosuccinate lyase

A0A384E0N4

Homo sapiens neanderthalensis (Neanderthal)

4.3.2.2

Unannotated

Bifunctional purine biosynthesis protein PurH

P9WHM7

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

3.5.4.10, 2.1.2.3

Unannotated

IMP cyclohydrolase

O27099

Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)

3.5.4.10

Unannotated

Phosphoribosyl isomerase A

P16250

Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)

5.3.1.24, 5.3.1.16

Unannotated

Phosphoribosylaminoimidazole-succinocarboxamide synthase

P27616

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

6.3.2.6

Unannotated

5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase

Q8U0R7

Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

6.3.4.23

Unannotated

Page Size:

1 to 10 of 14

Page 1 of 2

Protein name

Bifunctional purine biosynthesis protein ATIC

PDB-KB Proteins

P31335

EC number

3.5.4.10, 2.1.2.3

Ligand annotation

Unannotated

Total structures

Protein name

Bifunctional purine biosynthesis protein ATIC

PDB-KB Proteins

P31939

EC number

3.5.4.10, 2.1.2.3

Ligand annotation

Unannotated

Total structures

Protein name

Adenylosuccinate lyase

PDB-KB Proteins

A0A384E0N4

EC number

4.3.2.2

Ligand annotation

Unannotated

Total structures

Protein name

Bifunctional purine biosynthesis protein PurH

PDB-KB Proteins

P9WHM7

EC number

3.5.4.10, 2.1.2.3

Ligand annotation

Unannotated

Total structures

Protein name

5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase

PDB-KB Proteins

Q57600

EC number

6.3.4.23

Ligand annotation

Unannotated

Total structures

Items per page:

1 – 5 of 14

Interaction statistics

Interaction statistics shows the summary of aggregated protein-ligand interaction data of AMZ from 48 ligand instances in 13 distinct proteins and 23 PDB Structures. The protein-ligand interactions are computed using PDBe Arpeggio

Documentation

Ligand atoms

Sort by:

Amino acid properties

Interactions

Ligand interactions

Percentage of interactions by ligand atom compared to the total interactions of the ligand

Amino acid interactions

Percentage of interactions between ligand atom-amino acid pair compared to the total interactions of the amino acid

Icons:

Positively charged

Negatively charged

Polar

Hydrophobic

Aromatic

Aromatic (Trp)

Glycine

Cysteine

Proline

Atom-wise interactions of AMZ molecule
Percentage of interactions by ligand atom compared to the total interactions of the ligand

For full interaction statistics, including the heatmap showing ligand atom interaction frequency with different amino acids, please view on a larger screen