Protein profile

PA1584

succinate dehydrogenase iron-sulfur subunit

Genome: NC_002516.2

Gene: sdhB PA1584 Structure source: AlphaFold UniProt Q9I3D4
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Amino acids 235
Annotations 12
Features 19
PDB binders 44
Druggability 0.592

Overview

Basic information about this protein and its source genome.

Accession
PA1584
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
sdhB PA1584
Status
annotated
Amino acids
235
Structure source
AlphaFold
EC
1.3.5.1
GO
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: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: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:0046872 Binding to a metal ion.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
71.111
Human E-value
6.33e-45
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
CytoplasmicMembrane

Selected Druggability evidence

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 0.592
Structure –
Pocket –

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: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: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: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:0046872 Binding to a metal ion.
  • GO:0008177 Catalysis of the reaction: a quinone + succinate = a quinol + fumarate.
  • GO:0009060 The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor.
  • GO:0022904 A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
  • 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: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.

Sequence Features

Domain/signature hits from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
4 108 Pfam PF13085 2Fe-2S iron-sulfur cluster binding domain
4 108 InterPro IPR025192 Succinate dehydogenase/fumarate reductase N-terminal
3 231 PANTHER PTHR11921 SUCCINATE DEHYDROGENASE IRON-SULFUR PROTEIN
2 104 SUPERFAMILY SSF54292 2Fe-2S ferredoxin-like
2 104 InterPro IPR036010 2Fe-2S ferredoxin-like superfamily
1 104 Gene3D G3DSA:3.10.20.30 -
1 104 InterPro IPR012675 Beta-grasp domain superfamily
1 104 FunFam G3DSA:3.10.20.30:FF:000004 Succinate dehydrogenase iron-sulfur subunit
136 166 ProSiteProfiles PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
136 166 InterPro IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain
146 157 ProSitePatterns PS00198 4Fe-4S ferredoxin-type iron-sulfur binding region signature.
146 157 InterPro IPR017900 4Fe-4S ferredoxin, iron-sulphur binding, conserved site
6 227 NCBIfam TIGR00384 succinate dehydrogenase and fumarate reductase iron-sulfur protein
6 227 InterPro IPR004489 Succinate dehydrogenase/fumarate reductase iron-sulphur protein
105 232 SUPERFAMILY SSF46548 alpha-helical ferredoxin
105 235 Gene3D G3DSA:1.10.1060.10 -
105 235 InterPro IPR009051 Alpha-helical ferredoxin
145 218 Pfam PF13534 4Fe-4S dicluster domain
105 235 FunFam G3DSA:1.10.1060.10:FF:000001 Succinate dehydrogenase iron-sulfur subunit SdhB

3D Structure

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

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Structural evidence

0 + 1

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA1584
AlphaFold — — full sequence — Viewing
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
4 0.592
3 0.229
2 0.227

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.

94 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
1ZP0
Q007T0 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
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
1ZOY
Q007T0 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
1ZOY
Q007T0 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
3AE8
Q007T0 323.3 Da LogP 4.74 TPSA 38.3 ✓ Ro5 ✓ Clean CC(C)Oc1cccc(c1)NC(=O)c2ccccc2C(F)(F)F
FUM
3VRB
O44074 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
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
6MYO
Q9YHT2 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.