Protein profile

KP13_00511

Fumarate reductase subunit D

Genome: KpKP13

Gene: AHE46754.1 frdD Structure source: AlphaFold + ColabFold UniProt A0A0H3GH73
Export view
Amino acids 119
Annotations 5
Features 22
PDB binders 8
Druggability 0.786

Overview

Basic information about this protein and its source genome.

Accession
KP13_00511
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE46754.1 frdD
Status
annotated
Amino acids
119
Structure source
AlphaFold + ColabFold
GO
GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0006106 The chemical reactions and pathways involving fumarate, the anion of trans-1,2-ethenedicarboxylic acid, the diastereoisomer of maleate. It is a key intermediate in metabolism and is formed in the TCA cycle from succinate and converted into malate. GO:0045283 A membrane-bound flavoenzyme complex consisting of four subunits, A, B, C, and D. A and B comprise the membrane-extrinsic catalytic domain and C (InterPro:IPR003510; InterPro:IPR004224) and D (InterPro:IPR003418) link the catalytic centers to the electron-transport chain. This family consists of the 13 kDa hydrophobic subunit D. This component may be required to anchor the catalytic components of the fumarate reductase complex to the cytoplasmic membrane. Fumarate reductase couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, in a reaction opposite to that catalyzed by the related complex II of the respiratory chain (succinate dehydrogenase-(ubiquinone)). GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0000104 Catalysis of the reaction: succinate + acceptor = fumarate + reduced acceptor.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
50.427
DEG E-value
8.67e-37
Localization
CytoplasmicMembrane
ColabFold pLDDT
97.81

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.786
Structure A0A0H3GH73
Pocket Pocket 6
P2Rank 0.058
Structure A0A0H3GH73
Pocket Pocket 1
ColabFold model
FPocket 0.473 · Pocket 11
P2Rank 0.086 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 134 / 4744 genomes with a hit
Normalized 0.028

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0006106 The chemical reactions and pathways involving fumarate, the anion of trans-1,2-ethenedicarboxylic acid, the diastereoisomer of maleate. It is a key intermediate in metabolism and is formed in the TCA cycle from succinate and converted into malate.
  • GO:0045283 A membrane-bound flavoenzyme complex consisting of four subunits, A, B, C, and D. A and B comprise the membrane-extrinsic catalytic domain and C (InterPro:IPR003510; InterPro:IPR004224) and D (InterPro:IPR003418) link the catalytic centers to the electron-transport chain. This family consists of the 13 kDa hydrophobic subunit D. This component may be required to anchor the catalytic components of the fumarate reductase complex to the cytoplasmic membrane. Fumarate reductase couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, in a reaction opposite to that catalyzed by the related complex II of the respiratory chain (succinate dehydrogenase-(ubiquinone)).
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0000104 Catalysis of the reaction: succinate + acceptor = fumarate + reduced acceptor.

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records
Show feature table
Start End DB Term Name
1 119 SUPERFAMILY SSF81343 Fumarate reductase respiratory complex transmembrane subunits
1 119 InterPro IPR034804 Fumarate reductase/succinate dehydrogenase, transmembrane subunit
99 118 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
6 117 Pfam PF02313 Fumarate reductase subunit D
6 117 InterPro IPR003418 Fumarate reductase, subunit D
5 119 CDD cd00547 QFR_TypeD_subunitD
5 119 InterPro IPR003418 Fumarate reductase, subunit D
1 119 Gene3D G3DSA:1.20.1300.10 Fumarate reductase/succinate dehydrogenase, transmembrane subunit
79 98 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
62 84 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
99 118 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
119 119 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 119 FunFam G3DSA:1.20.1300.10:FF:000002 Fumarate reductase subunit D
44 54 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
20 42 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 119 PIRSF PIRSF000179 FrdD
1 119 InterPro IPR003418 Fumarate reductase, subunit D
6 119 Hamap MF_00709 Fumarate reductase subunit D [frdD].
6 119 InterPro IPR003418 Fumarate reductase, subunit D
12 43 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
55 78 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

Loading 3D structure...

Legend High Medium Low

Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GH73
AlphaFold — — full sequence — Viewing
ColabFold KP13_00511
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
6 0.786

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 3.72 0.142
2 0.81 0.003

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

58 records

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
BRS
1KFY
P0A8Q3 322.7 Da LogP 4.01 TPSA 106.5 ✓ Ro5 ✓ Clean C[C@H](c1ccc(cc1)Cl)c2cc(cc(c2O)[N+](=O)[O-])[N…
CE1
1KF6
P0A8Q3 538.8 Da LogP 4.03 TPSA 94.1 1 viol. ✓ Clean CCCCCCCCCCCCOCCOCCOCCOCCOCCOCCOCCOCCO
F3S
1KF6
P0A8Q3 295.8 Da LogP 2.59 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]2S[Fe]3[S]2[Fe]1S3
FES
1KF6
P0A8Q3 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
FLC
2B76
P0A8Q3 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
HQO
1KF6
P0A8Q3 259.3 Da LogP 3.69 TPSA 47.2 ✓ Ro5 Alert CCCCCCCc1cc(c2ccccc2[n+]1[O-])O
MQ7
1L0V
P0A8Q3 649.0 Da LogP 14.10 TPSA 34.1 2 viol. Alert CC1=C(C(=O)c2ccccc2C1=O)C\C=C(/C)\CC\C=C(/C)\CC…
OAA
1KF6
P0A8Q3 131.1 Da LogP -2.22 TPSA 94.5 ✓ Ro5 ✓ Clean C(C(=O)C(=O)O)C(=O)[O-]

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.