Protein profile

KP13_03280

Succinate dehydrogenase hydrophobic membrane anchor subunit

Genome: KpKP13

Gene: sdhD AHE45659.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GLI5

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Amino acids 115

Annotations 8

Features 21

PDB binders 11

Druggability 0.529

Overview

Basic information about this protein and its source genome.

Accession: KP13_03280
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: sdhD AHE45659.1
Status: annotated
Amino acids: 115
Structure source: AlphaFold + ColabFold

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0020037 Binding to a heme, a compound composed of iron complexed in a porphyrin (tetrapyrrole) ring. GO:0000104 Catalysis of the reaction: succinate + acceptor = fumarate + reduced acceptor. 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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. 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.

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 (%): 40.206
DEG E-value: 3.56e-17
Localization: CytoplasmicMembrane
ColabFold pLDDT: 95.77

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 0.529

Structure A0A0H3GLI5

Pocket Pocket 4

P2Rank 0.079

Structure A0A0H3GLI5

Pocket Pocket 1

ColabFold model

FPocket 0.743 · Pocket 2

P2Rank 0.094 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 120 / 4744 genomes with a hit

Normalized 0.025

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Gene Ontology (GO)

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
GO:0020037 Binding to a heme, a compound composed of iron complexed in a porphyrin (tetrapyrrole) ring.
GO:0000104 Catalysis of the reaction: succinate + acceptor = fumarate + reduced acceptor.
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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
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:0046872 Binding to a metal ion.
GO:0017004 The aggregation, arrangement and bonding together of a cytochrome complex. A cytochrome complex is a protein complex in which at least one of the proteins is a cytochrome, i.e. a heme-containing protein involved in catalysis of redox reactions.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records

Show feature table

Start	End	DB	Term	Name
1	115	PANTHER	PTHR38689	SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR SUBUNIT
1	115	InterPro	IPR014312	Succinate dehydrogenase, hydrophobic membrane anchor
10	113	NCBIfam	TIGR02968	succinate dehydrogenase, hydrophobic membrane anchor protein
10	113	InterPro	IPR014312	Succinate dehydrogenase, hydrophobic membrane anchor
81	91	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1	115	Gene3D	G3DSA:1.20.1300.10	Fumarate reductase/succinate dehydrogenase, transmembrane subunit
1	115	InterPro	IPR034804	Fumarate reductase/succinate dehydrogenase, transmembrane subunit
1	115	FunFam	G3DSA:1.20.1300.10:FF:000001	Succinate dehydrogenase hydrophobic membrane anchor subunit
5	115	SUPERFAMILY	SSF81343	Fumarate reductase respiratory complex transmembrane subunits
5	115	InterPro	IPR034804	Fumarate reductase/succinate dehydrogenase, transmembrane subunit
59	80	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
15	113	CDD	cd03494	SQR_TypeC_SdhD
1	16	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
40	58	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
91	113	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
1	115	PIRSF	PIRSF000169	SDH_D
114	115	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
17	39	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
92	113	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
16	38	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
48	70	TMHMM	TMhelix	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.

Loading 3D structure...

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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_A0A0H3GLI5	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_03280	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
4				0.529
3				0.016
1				0.001
2				0.0

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				3.01	0.079
2				0.66	0.001

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
2				0.743
1				0.235

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				3.74	0.143

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.

61 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
AT5	2ACZ	P0AC44	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)[…`
CBE	2WDQ	P0AC44	235.3 Da LogP 2.62 TPSA 38.3	✓ Ro5	✓ Clean	`CC1=C(SCCO1)C(=O)Nc2ccccc2`
CDN	1NEK	P0AC44	1151.5 Da LogP 14.77 TPSA 249.6	4 viol.	✓ Clean	`CCCCCCCCCCCCCCC(O)O[C@H](COC(CCCCC)O)CO[P@@](=O…`
DNT	1NEN	P0AC44	282.3 Da LogP 3.89 TPSA 106.5	✓ Ro5	✓ Clean	`CCCCCC(C)c1cc(cc(c1O)[N+](=O)[O-])[N+](=O)[O-]`
EPH	1NEK	P0AC44	709.9 Da LogP 10.16 TPSA 134.4	2 viol.	✓ Clean	`CCCC=CCC=CCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCC=CCC…`
F3S	1NEK	P0AC44	295.8 Da LogP 2.59 TPSA 0.0	✓ Ro5	✓ Clean	`S1[Fe]2S[Fe]3[S]2[Fe]1S3`
FES	1NEK	P0AC44	175.8 Da LogP 1.29 TPSA 0.0	✓ Ro5	✓ Clean	`S1[Fe]S[Fe]1`
OAA	1NEK	P0AC44	131.1 Da LogP -2.22 TPSA 94.5	✓ Ro5	✓ Clean	`C(C(=O)C(=O)O)C(=O)[O-]`
PCI	2WDR	P0AC44	266.3 Da LogP 4.66 TPSA 20.2	✓ Ro5	✓ Clean	`c1(c(c(c(c(c1Cl)Cl)Cl)Cl)Cl)O`
TEO	2WDQ	P0AC44	132.1 Da LogP -3.14 TPSA 103.7	✓ Ro5	✓ Clean	`C(=C(\O)/[O-])\[C@H](C(=O)[O-])O`
UQ2	1NEK	P0AC44	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`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC1529471	1.000	266.3 Da LogP 4.66 TPSA 20.2	✓ Ro5	✓ Clean	`Oc1c(Cl)c(Cl)c(Cl)c(Cl)c1Cl`
ZINC1532641	1.000	318.4 Da LogP 4.04 TPSA 52.6	✓ Ro5	Alert	`COC1=C(OC)C(=O)C(C/C=C(\C)CCC=C(C)C)=C(C)C1=O`
ZINC43478	1.000	235.3 Da LogP 2.62 TPSA 38.3	✓ Ro5	✓ Clean	`CC1=C(C(=O)Nc2ccccc2)SCCO1`
ZINC33649281	0.974	296.3 Da LogP 4.28 TPSA 106.5	✓ Ro5	✓ Clean	`CCCCCC[C@@H](C)c1cc([N+](=O)[O-])cc([N+](=O)[O-…`
ZINC33649283	0.974	296.3 Da LogP 4.28 TPSA 106.5	✓ Ro5	✓ Clean	`CCCCCC[C@H](C)c1cc([N+](=O)[O-])cc([N+](=O)[O-]…`
ZINC225408	0.900	247.9 Da LogP 3.71 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1c(Cl)c(Cl)c(O)c(Cl)c1Cl`
ZINC1583639	0.821	254.2 Da LogP 3.11 TPSA 106.5	✓ Ro5	✓ Clean	`CCC[C@@H](C)c1cc([N+](=O)[O-])cc([N+](=O)[O-])c…`
ZINC2038099	0.821	254.2 Da LogP 3.11 TPSA 106.5	✓ Ro5	✓ Clean	`CCC[C@H](C)c1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O`
ZINC154748	0.818	247.9 Da LogP 3.71 TPSA 40.5	✓ Ro5	Alert	`Oc1c(O)c(Cl)c(Cl)c(Cl)c1Cl`
ZINC1559692	0.750	250.3 Da LogP 2.32 TPSA 52.6	✓ Ro5	Alert	`COC1=C(OC)C(=O)C(CC=C(C)C)=C(C)C1=O`
ZINC13828017	0.725	240.2 Da LogP 2.72 TPSA 106.5	✓ Ro5	✓ Clean	`CC[C@@H](C)c1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O`
ZINC13828020	0.725	240.2 Da LogP 2.72 TPSA 106.5	✓ Ro5	✓ Clean	`CC[C@H](C)c1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O`
ZINC102190506	0.696	467.5 Da LogP 4.25 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OCCN)OC(=O)CC…`
ZINC102190512	0.696	467.5 Da LogP 4.25 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCCN)OC(=O)C…`
ZINC27416437	0.679	411.4 Da LogP 2.69 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCCN)OC(=O)CCCCC`
ZINC33902364	0.679	411.4 Da LogP 2.69 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCCN)OC(=O)CCC…`
ZINC2513914	0.675	235.3 Da LogP 2.62 TPSA 38.3	✓ Ro5	✓ Clean	`CC1=C(C(=O)Nc2ccccc2)OCCS1`
ZINC32918592	0.652	307.4 Da LogP 2.80 TPSA 64.6	✓ Ro5	✓ Clean	`CCOC(=O)c1ccc(NC(=O)C2=C(C)OCCS2)cc1`
ZINC1687159	0.625	226.2 Da LogP 2.33 TPSA 106.5	✓ Ro5	✓ Clean	`CC(C)c1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O`
ZINC9115226	0.625	360.5 Da LogP 3.64 TPSA 58.6	✓ Ro5	✓ Clean	`CC1=C(C(=O)Nc2ccc(C(=O)N3CCCCCC3)cc2)SCCO1`
ZINC1501016364	0.623	465.6 Da LogP 4.63 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O…`
ZINC20919537	0.612	388.5 Da LogP 4.46 TPSA 67.4	✓ Ro5	✓ Clean	`CC1=C(C(=O)Nc2ccc(C(=O)NC3CCCCCCC3)cc2)SCCO1`
ZINC9115252	0.612	374.5 Da LogP 4.07 TPSA 67.4	✓ Ro5	✓ Clean	`CC1=C(C(=O)Nc2ccc(C(=O)NC3CCCCCC3)cc2)SCCO1`
ZINC9115309	0.612	360.5 Da LogP 3.68 TPSA 67.4	✓ Ro5	✓ Clean	`CC1=C(C(=O)Nc2ccc(C(=O)NC3CCCCC3)cc2)SCCO1`
ZINC6895037	0.604	382.5 Da LogP 3.86 TPSA 67.4	✓ Ro5	✓ Clean	`CC1=C(C(=O)Nc2cccc(C(=O)NCc3ccccc3C)c2)SCCO1`
ZINC12323380	0.595	297.4 Da LogP 3.76 TPSA 38.3	✓ Ro5	✓ Clean	`O=C(Nc1ccccc1)C1=C(c2ccccc2)SCCO1`
ZINC6895073	0.588	374.5 Da LogP 3.57 TPSA 58.6	✓ Ro5	✓ Clean	`CC1=C(C(=O)Nc2ccc(CC(=O)N3CCCCCC3)cc2)SCCO1`
ZINC28404190	0.565	311.4 Da LogP 4.07 TPSA 38.3	✓ Ro5	✓ Clean	`Cc1ccc(NC(=O)C2=C(c3ccccc3)SCCO2)cc1`
ZINC98180109	0.563	246.9 Da LogP 3.59 TPSA 46.2	✓ Ro5	✓ Clean	`Nc1c(O)c(Cl)c(Cl)c(Cl)c1Cl`
ZINC1492540	0.558	355.8 Da LogP 3.84 TPSA 64.6	✓ Ro5	✓ Clean	`CC1=C(C(=O)Nc2ccc(Cl)c(C(=O)OC(C)C)c2)SCCO1`
ZINC13544781	0.556	482.6 Da LogP 4.22 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)OC[C@@H](CO[P@](=O)(O)OCC[N+](C)(C)C…`
ZINC13544783	0.556	482.6 Da LogP 4.22 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCC[N+](C)(C)C)…`
ZINC12322718	0.543	354.4 Da LogP 3.72 TPSA 67.4	✓ Ro5	✓ Clean	`CC(=O)Nc1ccc(NC(=O)C2=C(c3ccccc3)SCCO2)cc1`
ZINC13543439	0.540	454.5 Da LogP 3.44 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](CO[P@](=O)(O)OCC[N+](C)(C)C)…`
ZINC13543441	0.540	454.5 Da LogP 3.44 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCC[N+](C)(C)C)O…`
ZINC6894966	0.537	374.5 Da LogP 3.61 TPSA 67.4	✓ Ro5	✓ Clean	`CC1=C(C(=O)Nc2ccccc2C(=O)NCc2cccs2)SCCO1`
ZINC9115097	0.537	369.4 Da LogP 2.95 TPSA 80.3	✓ Ro5	✓ Clean	`CC1=C(C(=O)Nc2ccccc2C(=O)NCc2ccccn2)SCCO1`
ZINC129184	0.533	267.3 Da LogP 1.30 TPSA 72.5	✓ Ro5	✓ Clean	`CC1=C(C(=O)Nc2ccccc2)S(=O)(=O)CCO1`
ZINC102190945	0.525	411.5 Da LogP 3.29 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCCN`
ZINC32840692	0.525	425.5 Da LogP 3.68 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OCCN`
ZINC32840693	0.525	425.5 Da LogP 3.68 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OCCN`
ZINC32840704	0.525	453.6 Da LogP 4.46 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OCCN`
ZINC32840705	0.525	453.6 Da LogP 4.46 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OCCN`
ZINC95635984	0.525	397.4 Da LogP 2.90 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCCN`
ZINC102191119	0.524	498.6 Da LogP 3.65 TPSA 148.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@@H](O)CO…`
ZINC33822387	0.524	426.5 Da LogP 2.66 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCC(=O)OC[C@H](CO[P@@](=O)(O)OCC[N+](C)(C)C)O…`
ZINC33822389	0.524	426.5 Da LogP 2.66 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCC[N+](C)(C)C)…`
ZINC58649551	0.524	498.6 Da LogP 3.65 TPSA 148.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@H](O)CO)…`
ZINC5956205	0.524	212.2 Da LogP 1.77 TPSA 106.5	✓ Ro5	✓ Clean	`CCc1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O`
ZINC2046309	0.523	254.2 Da LogP 3.11 TPSA 106.5	✓ Ro5	✓ Clean	`CCC[C@H](C)c1cc([N+](=O)[O-])c(O)c([N+](=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.