Protein profile

KP13_05584

putative pyruvate-flavodoxin oxidoreductase

Genome: KpKP13

Gene: AHE44876.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GSL1

Export view

Amino acids 1175

Annotations 9

Features 52

PDB binders 6

Druggability 0.964

Overview

Basic information about this protein and its source genome.

Accession: KP13_05584
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE44876.1
Status: annotated
Amino acids: 1175
Structure source: AlphaFold + ColabFold

1.2.7.-

GO:0030976 Binding to thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases. GO:0022900 A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors. GO:0016903 Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor. 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:0005506 Binding to an iron (Fe) ion. GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: CytoplasmicMembrane
ColabFold pLDDT: 95.06

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 0.964

Structure A0A0H3GSL1

Pocket Pocket 1

P2Rank 0.895

Structure A0A0H3GSL1

Pocket Pocket 1

ColabFold model

FPocket 0.952 · Pocket 13

P2Rank 0.876 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 178 / 4744 genomes with a hit

Normalized 0.038

Sequence

Primary amino-acid sequence viewer.

MITIDGNGAVASVAFRTSEVIAIYPITPSSTMAEQADAWAGNGLKNVWGDVPRVVEMQSEAGAIGAVHGALQTGALSTSFTSSQGLLLMIPTLYKLAGQLMPFVLHVAARTVATHALSIFGDHSDVMAVRQTGCAMLCASSVQEAQDFALISHIATLQSRVPFIHFFDGFRTSHEINKIAPLADDTIRALLPQDKIAEHRQRALNPEHPVIRGTSANPDTYFQSREATNPWYDAVYDHVEKAMDDFAAATGRQYKPFEFYGHPQAERVIVIMGSAIGTCEEVVDELLSRGEKVGVLKVRLYRPFSAAHLLAALPESARAVAVLDRTKEPGALAEPLYLDVMTALAEAFNRGERETLPRTIGGRYGLSSKEFGPECVLAIFSELQAAQPKPRFTVGIYDDVTNLSLPLGENTLPAEAKLEALFYGLGSDGSVSATKNNIKIIGNSTPWFSQGYFVYDSKKAGGLTVSHLRVSEKPIRSSYLISQADFVGCHQLQFIDKYQMAERLKPGGIFLLNTPYSAVEVWSRLPQEVQATLNQKKARFYVVNAAKIARECSLGARINTVMQMAFFHLTQILPGDSALAELQAAIAKSYSSKGQELVERNWQALALARESLAEVPLQPVNASSPNRPPVVSDAAPDFVKTVTAAMLAGLGDALPVSALPPDGTWPMGTTRWEKRNIAEEIPIWKEALCTQCNHCVAACPHSAIRAKVVAPEEMENAPASLHSLDVKSRDMRGQKYVLQVAPEDCTGCNLCVEVCPAKDRQNPEIKAINMMSRLEHVEEEKVNYEYFLNLPEIDRSKLERIDIRTSQLISPLFEYSGACSGCGETPYIKLLTQLYGDRMLIANATGCSSIYGGNLPSTPYTTDANGRGPAWANSLFEDNAEFGLGFRLTVDQHRQRVMRLLSEFADKLPVELNAALHAEATPEVRREQVAALRQALAGVAGAEELLTDADALVEKSVWLIGGDGWAYDIGFGGLDHVLSLTENVNILVLDTQCYSNTGGQASKATPLGAVTKFGEHGKRKARKDLGVSMMMYGHVYVAQISLGAQLNQTVKAIQEAEAYPGPSLIIAYSPCEEHGYDLALSHDQMRQLTATGFWPLYRFDPRRADEGKIPLALDSRPPSDALAETLLNEQRFRRLNAQQPEVAEQLWKDAAADLQKRYDFLAQLAGKAEKSPSEG

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1.2.7.-

Gene Ontology (GO)

GO:0030976 Binding to thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.
GO:0022900 A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors.
GO:0016903 Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
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:0005506 Binding to an iron (Fe) ion.
GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
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:0006979 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.

Sequence Features

Domain/signature hits from InterPro and related databases.

52 records

Show feature table

Start	End	DB	Term	Name
736	765	ProSiteProfiles	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
736	765	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain
631	668	Gene3D	G3DSA:4.10.780.10	-
631	668	InterPro	IPR037112	Pyruvate-flavodoxin oxidoreductase, EKR domain superfamily
669	791	Gene3D	G3DSA:3.30.70.20	-
680	709	ProSiteProfiles	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
680	709	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain
6	169	CDD	cd07034	TPP_PYR_PFOR_IOR-alpha_like
6	169	InterPro	IPR002880	Pyruvate flavodoxin/ferredoxin oxidoreductase, pyrimidine binding domain
2	254	SUPERFAMILY	SSF52518	Thiamin diphosphate-binding fold (THDP-binding)
2	254	InterPro	IPR029061	Thiamin diphosphate-binding fold
665	838	SUPERFAMILY	SSF54862	4Fe-4S ferredoxins
1	1164	PANTHER	PTHR32154	PYRUVATE-FLAVODOXIN OXIDOREDUCTASE-RELATED
255	414	Gene3D	G3DSA:3.40.50.920	-
255	414	InterPro	IPR009014	Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II
419	668	SUPERFAMILY	SSF53323	Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
419	668	InterPro	IPR002869	Pyruvate-flavodoxin oxidoreductase, central domain
1	1165	NCBIfam	TIGR02176	pyruvate:ferredoxin (flavodoxin) oxidoreductase
1	1165	InterPro	IPR011895	Pyruvate-flavodoxin oxidoreductase
1	1174	PIRSF	PIRSF000159	NifJ
1	1174	InterPro	IPR011895	Pyruvate-flavodoxin oxidoreductase
417	623	Gene3D	G3DSA:3.40.920.10	-
417	623	InterPro	IPR002869	Pyruvate-flavodoxin oxidoreductase, central domain
1	254	Gene3D	G3DSA:3.40.50.970	-
689	757	Pfam	PF12838	4Fe-4S dicluster domain
689	757	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain
1	254	FunFam	G3DSA:3.40.50.970:FF:000012	Pyruvate:ferredoxin (Flavodoxin) oxidoreductase
426	610	Pfam	PF01558	Pyruvate ferredoxin/flavodoxin oxidoreductase
426	610	InterPro	IPR019752	Pyruvate/ketoisovalerate oxidoreductase, catalytic domain
811	1166	CDD	cd03377	TPP_PFOR_PNO
794	1167	Gene3D	G3DSA:3.40.50.970	-
669	791	FunFam	G3DSA:3.30.70.20:FF:000022	Pyruvate:ferredoxin (Flavodoxin) oxidoreductase
794	1166	SUPERFAMILY	SSF52518	Thiamin diphosphate-binding fold (THDP-binding)
794	1166	InterPro	IPR029061	Thiamin diphosphate-binding fold
255	411	SUPERFAMILY	SSF52922	TK C-terminal domain-like
255	411	InterPro	IPR009014	Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II
622	679	SMART	SM00890	EKR_2
622	679	InterPro	IPR019456	Pyruvate-flavodoxin oxidoreductase, EKR domain
265	347	Pfam	PF17147	Pyruvate:ferredoxin oxidoreductase core domain II
265	347	InterPro	IPR033412	Pyruvate:ferredoxin oxidoreductase, core domain II
13	243	Pfam	PF01855	Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
13	243	InterPro	IPR002880	Pyruvate flavodoxin/ferredoxin oxidoreductase, pyrimidine binding domain
255	413	FunFam	G3DSA:3.40.50.920:FF:000007	Pyruvate:ferredoxin (Flavodoxin) oxidoreductase
631	668	FunFam	G3DSA:4.10.780.10:FF:000001	Probable pyruvate-flavodoxin oxidoreductase
626	678	Pfam	PF10371	Domain of unknown function
626	678	InterPro	IPR019456	Pyruvate-flavodoxin oxidoreductase, EKR domain
745	756	ProSitePatterns	PS00198	4Fe-4S ferredoxin-type iron-sulfur binding region signature.
745	756	InterPro	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site
794	1167	FunFam	G3DSA:3.40.50.970:FF:000047	Probable pyruvate-flavodoxin oxidoreductase
416	626	FunFam	G3DSA:3.40.920.10:FF:000001	Pyruvate:ferredoxin (Flavodoxin) oxidoreductase
936	1066	Pfam	PF02775	Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
936	1066	InterPro	IPR011766	Thiamine pyrophosphate enzyme, TPP-binding

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...

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_A0A0H3GSL1	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_05584	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				0.964
78				0.361
5				0.205

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	Score	Probability
1	18.61	0.826
2	10.75	0.577
3	5.68	0.275
4	5.5	0.263
5	5.45	0.259

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
13				0.952

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	Score	Probability
1	15.83	0.763
2	9.67	0.52
3	8.25	0.439
4	7.38	0.386
5	7.06	0.366

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.

9 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
5SR	5EXE	Q2RI41	468.3 Da LogP -0.09 TPSA 209.1	✓ Ro5	✓ Clean	`Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(=O)O)CCOP(=O)(O)OP…`
CO2	1KEK	P94692	44.0 Da LogP -0.58 TPSA 34.1	✓ Ro5	✓ Clean	`C(=O)=O`
HTL	1KEK	P94692	467.4 Da LogP 1.04 TPSA 186.0	✓ Ro5	✓ Clean	`Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(=O)C)CCO[P@@](=O)(…`
O2T	5EXD	Q2RI41	514.3 Da LogP -1.57 TPSA 249.6	3 viol.	✓ Clean	`Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(C(=O)O)(O)O)CCOP(=…`
PYR	2C42	P94692	88.1 Da LogP -0.34 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)C(=O)O`
TDL	6CIO	Q2RMD6	513.4 Da LogP 0.13 TPSA 226.5	2 viol.	✓ Clean	`Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@](C)(C(=O)O)O)CCO…`

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
ZINC8215517	0.656	425.3 Da LogP 0.84 TPSA 169.0	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCO[P@@](=O)(O)OP(=O)(O)O)c2C)…`
ZINC1532839	0.522	345.3 Da LogP 0.72 TPSA 122.4	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCOP(=O)(O)O)c2C)c(N)n1`
ZINC13540298	0.507	440.3 Da LogP 0.72 TPSA 187.1	✓ Ro5	✓ Clean	`Cc1ncc(Cn2c(C)c(CCO[P@@](=O)(O)OP(=O)(O)O)sc2=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.