PDBe-KB Ligand Pages (PDBeChem)

Examples: STI GLC NAG HEM CLC_000191 PRD_000468

FLC

CITRATE ANION

Description

Synonyms

CITRATE ANION

Formula

C6 H5 O7

IUPAC InChI

InChI=1S/C6H8O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12)/p-3

IUPAC InChIKey

KRKNYBCHXYNGOX-UHFFFAOYSA-K

SMILES

C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O

Source OpenEye

Is part of

CLC_002284.

First observed in

1b0k

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

Atom labelled FLC

Physicochemical properties

Molecular properties

Molecular weight

Total mass of the molecule in Daltons

189.0 Da

Labute accessible surface area

Accessible surface area according to the Labute's definition

79.3 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

29.2

Wildman-Crippen Log P

Octanol/Water partition coefficient predicted using Wildman-Crippen method

-5.3

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

140.6

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 472 distinct proteins and 713 PDB Structures. Group data by:

Proteins

Structures

1 to 10 of 473. Page 1 of 48

Protein name

Protein Overview

Total structures

Organism

EC number

Ligand function

Unmapped

Unannotated

Xaa-Pro aminopeptidase

P15034

Escherichia coli (strain K12)

3.4.11.9

Unannotated

ATP-citrate synthase

P53396

Homo sapiens (Human)

2.3.3.8

Unannotated

Pantothenate kinase

P9WPA7

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

2.7.1.33

Unannotated

Diacylglycerol kinase

P0ABN1

Escherichia coli (strain K12)

2.7.1.107

Unannotated

Ribonuclease TTHA0252

Q5SLP1

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

3.1.-.-

Unannotated

Malto-oligosyltrehalose trehalohydrolase

Q55088

Saccharolobus solfataricus

3.2.1.141

Unannotated

Urokinase-type plasminogen activator

P00749

Homo sapiens (Human)

3.4.21.73

Unannotated

Ribonuclease pancreatic

P61823

Bos taurus (Bovine)

4.6.1.18

Unannotated

Protein RecA

P9WHJ3

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

3.1.-.-

Unannotated

Page Size:

1 to 10 of 473

Page 1 of 48

Protein name

---

PDB-KB Proteins

EC number

---

Ligand annotation

Unannotated

Total structures

Protein name

Serine/threonine-protein phosphatase

PDB-KB Proteins

C4YM68

EC number

3.1.3.16

Ligand annotation

Unannotated

Total structures

Protein name

Bacterial microcompartment shell protein EutK

PDB-KB Proteins

P76540

EC number

---

Ligand annotation

Unannotated

Total structures

Protein name

Alpha-amylase

PDB-KB Proteins

U5CJP3

EC number

3.2.1.1

Ligand annotation

Unannotated

Total structures

Protein name

EKC/KEOPS complex subunit TP53RK

PDB-KB Proteins

Q96S44

EC number

3.6.-.-, 2.7.11.1

Ligand annotation

Unannotated

Total structures

Items per page:

1 – 5 of 473

Interaction statistics

Interaction statistics shows the summary of aggregated protein-ligand interaction data of FLC from 1311 ligand instances in 473 PDB structures and 713 PDB chains. 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 FLC 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