PDBe-KB Ligand Pages (PDBeChem)

Examples: STI GLC NAG HEM CLC_000191 PRD_000468

A

ADENOSINE-5'-MONOPHOSPHATE

Description

Synonyms

AMP, PAdo, Ado5'P, 5'-AMP, My-B-Den, Adenylate, Adenylic aci...Show more

Formula

C10 H14 N5 O7 P

Standard InChI

InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,1...Show more

Standard InChI Key

UDMBCSSLTHHNCD-KQYNXXCUSA-N

SMILES

c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O...Show more

Source OpenEye

Is part of

A1II9 CLC_001840 CLC_002159 CLC_002440 CLC_002821 CLC_003113 CLC_003260 CLC_003311 CLC_003312 CLC_003419 CLC_003420 CLC_003424 PRD_002431.

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 / 2

Physicochemical properties

Molecular properties

Molecular weight

Total mass of the molecule in Daltons

347.1 Da

Labute accessible surface area

Accessible surface area according to the Labute's definition

148.4 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

0.5

Wildman-Crippen molar refractivity

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

70.6

Wildman-Crippen Log P

Octanol/Water partition coefficient predicted using Wildman-Crippen method

-2.7

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

186.1

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 15 distinct proteins and 7 PDB Structures. Group data by:

Proteins

Structures

Protein name

Protein Overview

Total structures

Organism

EC number

Ligand function

Unmapped

Unannotated

Large ribosomal subunit protein bL32m

Q9BYC8

Homo sapiens (Human)

Unannotated

Large ribosomal subunit protein bL36m

Q9P0J6

Homo sapiens (Human)

Unannotated

Uncharacterized protein

Q9X1T1

Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Unannotated

Large ribosomal subunit protein uL14m

Q6P1L8

Homo sapiens (Human)

Unannotated

Large ribosomal subunit protein uL3m

P09001

Homo sapiens (Human)

Unannotated

Mitochondrial ribosome-associated GTPase 1

Q9BT17

Homo sapiens (Human)

Unannotated

Translation initiation factor IF-3

Q5SKU2

Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Unannotated

Large ribosomal subunit protein bL19m

P49406

Homo sapiens (Human)

Unannotated

Large ribosomal subunit protein bL17m

Q9NRX2

Homo sapiens (Human)

Unannotated

Page Size:

1 to 10 of 16

Page 1 of 2

Protein name

Large ribosomal subunit protein bL32m

PDB-KB Proteins

Q9BYC8

EC number

---

Ligand annotation

Unannotated

Total structures

Protein name

---

PDB-KB Proteins

EC number

---

Ligand annotation

Unannotated

Total structures

Protein name

Large ribosomal subunit protein bL36m

PDB-KB Proteins

Q9P0J6

EC number

---

Ligand annotation

Unannotated

Total structures

Protein name

Uncharacterized protein

PDB-KB Proteins

Q9X1T1

EC number

---

Ligand annotation

Unannotated

Total structures

Protein name

Large ribosomal subunit protein uL14m

PDB-KB Proteins

Q6P1L8

EC number

---

Ligand annotation

Unannotated

Total structures

Items per page:

1 – 5 of 16

Interaction statistics

Interaction statistics shows the summary of aggregated protein-ligand interaction data of A from 91 ligand instances in 15 distinct proteins and 7 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 A 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