Protein profile

KP13_00513

Fumarate reductase iron-sulfur subunit

Genome: KpKP13

Gene: AHE46752.1 frdB Structure source: AlphaFold + ColabFold UniProt A0A0H3GM87
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Amino acids 244
Annotations 12
Features 24
PDB binders 47
Druggability 0.508

Overview

Basic information about this protein and its source genome.

Accession
KP13_00513
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE46752.1 frdB
Status
annotated
Amino acids
244
Structure source
AlphaFold + ColabFold
EC
1.3.5.1
GO
GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. GO:0009055 A molecular function representing the directed movement of electrons from one molecular entity to another, typically mediated by electron carriers or acceptors, resulting in the transfer of energy and/or the reduction-oxidation (redox) transformation of chemical species. This activity is fundamental to various biological processes, including cellular respiration and photosynthesis, as well as numerous enzymatic reactions involved in metabolic pathways. GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms. GO:0006099 A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle. GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands. GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
37.209
Human E-value
8.45e-11
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
CytoplasmicMembrane
ColabFold pLDDT
96.64

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 0.508
Structure A0A0H3GM87
Pocket Pocket 1
P2Rank 0.078
Structure A0A0H3GM87
Pocket Pocket 1
ColabFold model
FPocket 0.185 · Pocket 8
P2Rank 0.016 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 157 / 4744 genomes with a hit
Normalized 0.033

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 11 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

11
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
  • GO:0009055 A molecular function representing the directed movement of electrons from one molecular entity to another, typically mediated by electron carriers or acceptors, resulting in the transfer of energy and/or the reduction-oxidation (redox) transformation of chemical species. This activity is fundamental to various biological processes, including cellular respiration and photosynthesis, as well as numerous enzymatic reactions involved in metabolic pathways.
  • GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • GO:0006099 A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
  • GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • 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:0051538 Binding to a 3 iron, 4 sulfur (3Fe-4S) cluster; this cluster consists of three iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. It is essentially a 4Fe-4S cluster with one iron missing.
  • GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0046872 Binding to a metal ion.
  • GO:0008177 Catalysis of the reaction: a quinone + succinate = a quinol + fumarate.
  • GO:0009061 The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor.

Sequence Features

Domain/signature hits from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
11 229 NCBIfam TIGR00384 succinate dehydrogenase and fumarate reductase iron-sulfur protein
11 229 InterPro IPR004489 Succinate dehydrogenase/fumarate reductase iron-sulphur protein
58 66 ProSitePatterns PS00197 2Fe-2S ferredoxin-type iron-sulfur binding region signature.
58 66 InterPro IPR006058 2Fe-2S ferredoxin, iron-sulphur binding site
146 219 Pfam PF13183 4Fe-4S dicluster domain
146 219 InterPro IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain
3 106 FunFam G3DSA:3.10.20.30:FF:000009 Succinate dehydrogenase iron-sulfur subunit
8 111 Pfam PF13085 2Fe-2S iron-sulfur cluster binding domain
8 111 InterPro IPR025192 Succinate dehydogenase/fumarate reductase N-terminal
23 243 PANTHER PTHR43551 FUMARATE REDUCTASE IRON-SULFUR SUBUNIT
149 160 ProSitePatterns PS00198 4Fe-4S ferredoxin-type iron-sulfur binding region signature.
149 160 InterPro IPR017900 4Fe-4S ferredoxin, iron-sulphur binding, conserved site
107 229 SUPERFAMILY SSF46548 alpha-helical ferredoxin
140 169 ProSiteProfiles PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
140 169 InterPro IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain
7 97 ProSiteProfiles PS51085 2Fe-2S ferredoxin-type iron-sulfur binding domain profile.
7 97 InterPro IPR001041 2Fe-2S ferredoxin-type iron-sulfur binding domain
3 106 Gene3D G3DSA:3.10.20.30 -
3 106 InterPro IPR012675 Beta-grasp domain superfamily
107 244 FunFam G3DSA:1.10.1060.10:FF:000002 Succinate dehydrogenase iron-sulfur subunit
107 244 Gene3D G3DSA:1.10.1060.10 -
107 244 InterPro IPR009051 Alpha-helical ferredoxin
4 106 SUPERFAMILY SSF54292 2Fe-2S ferredoxin-like
4 106 InterPro IPR036010 2Fe-2S ferredoxin-like superfamily

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

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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_A0A0H3GM87
AlphaFold — — full sequence — Viewing
ColabFold KP13_00513
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
1 0.508

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 2.68 0.08
2 2.59 0.074
3 0.91 0.004

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.

97 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
11J
3AEG
Q007T0 399.2 Da LogP 5.21 TPSA 29.1 1 viol. ✓ Clean c1ccc(cc1)c2cccc(c2)NC(=O)c3ccccc3I
12J
4YSZ
O44074 381.2 Da LogP 4.33 TPSA 38.3 ✓ Ro5 ✓ Clean CC(C)Oc1cccc(c1)NC(=O)c2ccccc2I
3NP
3P4S
P0AC47 119.1 Da LogP -0.26 TPSA 80.4 ✓ Ro5 ✓ Clean C(C[N+](=O)[O-])C(=O)O
3PE
6MYO
Q9YHT2 748.1 Da LogP 12.06 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN)OC…
4YP
5C2T
O44074 303.4 Da LogP 3.35 TPSA 69.4 ✓ Ro5 Alert CC1=C(C(=O)C(=C(C1=O)N)OC)C/C=C(\C)/CCC=C(C)C
AT5
3AEE
Q007T0 366.2 Da LogP 2.79 TPSA 88.6 ✓ Ro5 ✓ Clean C[C@@H](C[C@H](C)C(=O)C1=C(C(=C(NC1=O)OC)OC)O)[…
BOL
3AED
Q007T0 323.1 Da LogP 3.54 TPSA 29.1 ✓ Ro5 ✓ Clean c1ccc(cc1)NC(=O)c2ccccc2I
BRS
1KFY
P0AC47 322.7 Da LogP 4.01 TPSA 106.5 ✓ Ro5 ✓ Clean C[C@H](c1ccc(cc1)Cl)c2cc(cc(c2O)[N+](=O)[O-])[N…
CBE
2WDQ
P07014 235.3 Da LogP 2.62 TPSA 38.3 ✓ Ro5 ✓ Clean CC1=C(SCCO1)C(=O)Nc2ccccc2
CDN
1NEK
P07014 1151.5 Da LogP 14.77 TPSA 249.6 4 viol. ✓ Clean CCCCCCCCCCCCCCC(O)O[C@H](COC(CCCCC)O)CO[P@@](=O…
CE1
1KF6
P0AC47 538.8 Da LogP 4.03 TPSA 94.1 1 viol. ✓ Clean CCCCCCCCCCCCOCCOCCOCCOCCOCCOCCOCCOCCO
DMW
2BS4
P17596 186.2 Da LogP 2.40 TPSA 34.1 ✓ Ro5 Alert CC1=C(C(=O)c2ccccc2C1=O)C
DNT
1NEN
P07014 282.3 Da LogP 3.89 TPSA 106.5 ✓ Ro5 ✓ Clean CCCCCC(C)c1cc(cc(c1O)[N+](=O)[O-])[N+](=O)[O-]
E23
4YTP
Q007T0 335.4 Da LogP 4.93 TPSA 29.1 ✓ Ro5 ✓ Clean CC(C)(C)c1ccc(cc1)CNC(=O)c2ccccc2C(F)(F)F
E24
4YSY
O44074 348.2 Da LogP 4.94 TPSA 29.1 ✓ Ro5 ✓ Clean c1ccc(c(c1)C(=O)NCc2ccc(cc2Cl)Cl)C(F)(F)F
EBM
3AEC
Q007T0 289.1 Da LogP 2.43 TPSA 29.1 ✓ Ro5 ✓ Clean CC(C)NC(=O)c1ccccc1I
EPH
1ZOY
Q007T0 709.9 Da LogP 10.16 TPSA 134.4 2 viol. ✓ Clean CCCC=CCC=CCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCC=CCC…
F3S
1KF6
P0AC47 295.8 Da LogP 2.59 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]2S[Fe]3[S]2[Fe]1S3
F6A
3ABV
Q007T0 341.3 Da LogP 5.62 TPSA 29.1 1 viol. ✓ Clean c1ccc(cc1)c2cccc(c2)NC(=O)c3ccccc3C(F)(F)F
F7A
3AEB
Q007T0 357.3 Da LogP 5.75 TPSA 38.3 1 viol. ✓ Clean c1ccc(cc1)Oc2cccc(c2)NC(=O)c3ccccc3C(F)(F)F
F9A
3AEA
Q007T0 322.3 Da LogP 4.02 TPSA 32.3 ✓ Ro5 ✓ Clean CN(C)Cc1cccc(c1)NC(=O)c2ccccc2C(F)(F)F
FD8
3AE9
Q007T0 447.3 Da LogP 6.45 TPSA 38.3 1 viol. ✓ Clean c1ccc(c(c1)C(=O)Nc2cccc(c2)Oc3c(c(c(c(c3F)F)F)F…
FES
1KF6
P0AC47 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
FLC
2B76
P0AC47 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
FTN
6MYO
Q9YHT2 323.3 Da LogP 4.74 TPSA 38.3 ✓ Ro5 ✓ Clean CC(C)Oc1cccc(c1)NC(=O)c2ccccc2C(F)(F)F
FUM
3P4P
P0AC47 116.1 Da LogP -0.29 TPSA 74.6 ✓ Ro5 ✓ Clean C(=C/C(=O)O)\C(=O)O
GUA
3P4R
P0AC47 132.1 Da LogP 0.33 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)CC(=O)O
HQO
1KF6
P0AC47 259.3 Da LogP 3.69 TPSA 47.2 ✓ Ro5 Alert CCCCCCCc1cc(c2ccccc2[n+]1[O-])O
JMP
3AE6
Q007T0 299.3 Da LogP 3.42 TPSA 75.6 ✓ Ro5 ✓ Clean CC(C)Oc1cccc(c1)NC(=O)c2ccccc2C(=O)O
LMT
1E7P
P17596 510.6 Da LogP -0.45 TPSA 178.5 3 viol. ✓ Clean CCCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1…
MLA
1E7P
P17596 104.1 Da LogP -0.45 TPSA 74.6 ✓ Ro5 ✓ Clean C(C(=O)O)C(=O)O
MLI
3ABV
Q007T0 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
MQ7
1L0V
P0AC47 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…
MRN
3AE5
Q007T0 269.3 Da LogP 4.03 TPSA 38.3 ✓ Ro5 ✓ Clean Cc1ccccc1C(=O)Nc2cccc(c2)OC(C)C
N1M
3AE4
Q007T0 261.1 Da LogP 1.65 TPSA 29.1 ✓ Ro5 ✓ Clean CNC(=O)c1ccccc1I
NBI
3AE3
Q007T0 242.2 Da LogP 2.85 TPSA 72.2 ✓ Ro5 ✓ Clean c1ccc(cc1)NC(=O)c2ccccc2[N+](=O)[O-]
OAA
1KF6
P0AC47 131.1 Da LogP -2.22 TPSA 94.5 ✓ Ro5 ✓ Clean C(C(=O)C(=O)O)C(=O)[O-]
PCI
3SFD
Q007T0 266.3 Da LogP 4.66 TPSA 20.2 ✓ Ro5 ✓ Clean c1(c(c(c(c(c1Cl)Cl)Cl)Cl)Cl)O
RQX
3VR8
O44074 263.3 Da LogP 2.41 TPSA 69.4 ✓ Ro5 Alert CCC/C(=C/CC1=C(C(=O)C(=C(C1=O)OC)N)C)/C
SLI
3AE2
Q007T0 213.2 Da LogP 2.64 TPSA 49.3 ✓ Ro5 ✓ Clean c1ccc(cc1)NC(=O)c2ccccc2O
TEO
2WDQ
P07014 132.1 Da LogP -3.14 TPSA 103.7 ✓ Ro5 ✓ Clean C(=C(\O)/[O-])\[C@H](C(=O)[O-])O
TFZ
3AE1
Q007T0 265.2 Da LogP 3.96 TPSA 29.1 ✓ Ro5 ✓ Clean c1ccc(cc1)NC(=O)c2ccccc2C(F)(F)F
TMG
3SFE
Q007T0 201.3 Da LogP 2.69 TPSA 41.6 ✓ Ro5 ✓ Clean c1ccc2c(c1)[nH]c(n2)c3cscn3
TTF
1ZP0
Q007T0 222.2 Da LogP 2.45 TPSA 34.1 ✓ Ro5 ✓ Clean c1cc(sc1)C(=O)CC(=O)C(F)(F)F
UMQ
6MYO
Q9YHT2 496.6 Da LogP -0.84 TPSA 178.5 2 viol. ✓ Clean CCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)…
UQ1
1ZOY
Q007T0 250.3 Da LogP 2.32 TPSA 52.6 ✓ Ro5 Alert CC1=C(C(=O)C(=C(C1=O)OC)OC)CC=C(C)C
UQ2
1NEK
P07014 318.4 Da LogP 4.04 TPSA 52.6 ✓ Ro5 Alert CC1=C(C(=O)C(=C(C1=O)OC)OC)C\C=C(/C)\CCC=C(C)C

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.