KpKP13 Protein target profile

Formate hydrogenlyase subunit 2

Accession: KP13_02573

Gene: hycB AHE43034.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GWP6

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Length 202

Pocket druggability (P2Rank · AlphaFold DB model) 0.065

Direct ligand evidence 0 58 total records

Functional annotation 0 EC 2 GO

Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Risks to review

Microbiome similarity 109 of 4744 screened genomes (2.3%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.28. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.07.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target: No hit
Gut microbiome similarity: 2.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT: 85.87 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.065

Structure A0A0H3GWP6

Pocket Pocket 1

Druggability (FPocket) 0.285

Structure A0A0H3GWP6

Pocket Pocket 6

ColabFold model

P2Rank 0.122 · Pocket 1

FPocket 0.336 · Pocket 17

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 109 / 4744 genomes with a hit

Prevalence 2.3%

Sequence

Primary amino-acid sequence viewer.

MNRFVIADSTVCIGCRTCEAACSETHRQHGLQAMPRLQVMRNEKESAPQMCHHCEDAPCATVCPVNAIQRVDGAVQLNESLCVSCKLCGIACPFGAIEFSGSRPLDIPANANTRLAPPAPPAPARVSSLLDWVPGVRAIAVKCDLCHFDDQGPACVRTCPTNALMLVDSRDIAQASKRKRQLTFNTDLGDLSLFQAQQGERE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Subcellular localization

Localization: Cytoplasmic

Gene Ontology (GO)

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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records

Show feature table

Start	End	DB	Term	Name
16	20	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
1	20	Phobius	SIGNAL_PEPTIDE	Signal peptide region
34	106	FunFam	G3DSA:3.30.70.20:FF:000036	4Fe-4S dicluster domain-containing protein
1	70	Gene3D	G3DSA:3.30.70.20	-
73	102	ProSiteProfiles	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
73	102	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain
1	3	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
73	191	Gene3D	G3DSA:3.30.70.20	-
4	167	CDD	cd10554	HycB_like
82	93	ProSitePatterns	PS00198	4Fe-4S ferredoxin-type iron-sulfur binding region signature.
82	93	InterPro	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site
1	184	PANTHER	PTHR42859	OXIDOREDUCTASE
21	202	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
47	97	Pfam	PF13247	4Fe-4S dicluster domain
47	97	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain
2	32	ProSiteProfiles	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
2	32	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain
1	182	SUPERFAMILY	SSF54862	4Fe-4S ferredoxins
4	15	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low

How colors and pocket overlays are used

Uniform protein color marks the displayed model as a single molecular object.

Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.

Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.

'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.

'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.

'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.

Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1

0.065

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Surrounding area

Pocket 2 P2Rank #2

0.056

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Surrounding area

Pocket 3 P2Rank #3

0.045

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Surrounding area

Pocket 4 P2Rank #4

0.023

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Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #6

0.285

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Surrounding area

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1

0.122

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Surrounding area

Pocket 2 P2Rank #2

0.082

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Surrounding area

Pocket 3 P2Rank #3

0.05

Likely same site as FPocket 2 1.0 Å 4 shared residues 100% of smaller site

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Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #17

0.336

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Surrounding area

Pocket 2 FPocket #4

0.332

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Surrounding area

Pocket 3 FPocket #2

0.296

Likely same site as P2Rank 3 1.0 Å 4 shared residues 100% of smaller site

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Surrounding area

All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold DB AF_A0A0H3GWP6	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_02573	ColabFold	—	—	full sequence	—	Loaded

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

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 8 records from similar proteins

Structural ligands 8 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

F3S PDB via homolog 295.8 Da · LogP 2.59 · TPSA 0.0 Open detail RCSB PDB

MGD PDB via homolog Detail RCSB PDB

MO PDB via homolog Detail RCSB PDB

O PDB via homolog Detail RCSB PDB

PG5 PDB via homolog Detail RCSB PDB

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, 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
F3S RCSB PDB	6F0K	D0MDD5	295.8 Da LogP 2.59 TPSA 0.0	✓ Ro5	✓ Clean	`S1[Fe]2S[Fe]3[S]2[Fe]1S3`
MGD RCSB PDB	6CZ8	Q7WTT9	740.6 Da LogP -2.06 TPSA 346.6	3 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=…`
MO RCSB PDB	6CZ8	Q7WTT9	95.9 Da LogP -0.00 TPSA 0.0	✓ Ro5	✓ Clean	`[Mo]`
O RCSB PDB	6CZ8	Q7WTT9	18.0 Da LogP -0.82 TPSA 31.5	✓ Ro5	✓ Clean	`O`
PG5 RCSB PDB	6CZ8	Q7WTT9	178.2 Da LogP 0.31 TPSA 36.9	✓ Ro5	✓ Clean	`COCCOCCOCCOC`
PTE RCSB PDB	6X1O	I6U881	1024.8 Da LogP 0.35 TPSA 361.4	3 viol.	✓ Clean	`C1[C@@H]2C3=C([C@H]4[C@@H](O2)NC5=C(N4)C(=O)NC(…`
TAU RCSB PDB	6X6U	I6U881	125.1 Da LogP -1.17 TPSA 80.4	✓ Ro5	✓ Clean	`C(CS(=O)(=O)O)N`
UKM RCSB PDB	6X1O	I6U881	154.2 Da LogP -0.01 TPSA 74.6	✓ Ro5	✓ Clean	`CCC[C@H](O)S(=O)(=O)O`

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
ZINC1692489 ZINC	1.000	222.3 Da LogP 0.33 TPSA 46.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOC`
ZINC4530388 ZINC	1.000	266.3 Da LogP 0.35 TPSA 55.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOC`
ZINC5701172 ZINC	1.000	310.4 Da LogP 0.36 TPSA 64.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOC`
ZINC5997861 ZINC	1.000	398.5 Da LogP 0.40 TPSA 83.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOC`
ZINC34764844 ZINC	0.733	206.3 Da LogP 1.09 TPSA 36.9	✓ Ro5	✓ Clean	`CCCOCCOCCOCCOC`
ZINC140264883 ZINC	0.688	223.3 Da LogP -0.43 TPSA 72.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCON`
ZINC143705779 ZINC	0.688	443.5 Da LogP -0.34 TPSA 118.3	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCON`
ZINC1580161 ZINC	0.688	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118 ZINC	0.688	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257 ZINC	0.688	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC33358855 ZINC	0.688	207.3 Da LogP -0.36 TPSA 62.9	✓ Ro5	✓ Clean	`COCCOCCOCCOCCN`
ZINC34317654 ZINC	0.688	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44076059 ZINC	0.688	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44583772 ZINC	0.688	356.5 Da LogP 0.66 TPSA 64.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCS`
ZINC5024003 ZINC	0.688	251.3 Da LogP -0.34 TPSA 72.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCN`
ZINC5210101 ZINC	0.688	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC575432090 ZINC	0.688	355.4 Da LogP -0.38 TPSA 99.9	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCON`
ZINC575432265 ZINC	0.688	399.5 Da LogP -0.36 TPSA 109.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCON`
ZINC5997860 ZINC	0.688	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC71254558 ZINC	0.688	444.6 Da LogP 0.70 TPSA 83.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC71254563 ZINC	0.688	488.6 Da LogP 0.71 TPSA 92.3	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC80685077 ZINC	0.688	427.5 Da LogP -0.28 TPSA 109.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCN`
ZINC83253927 ZINC	0.688	400.5 Da LogP 0.68 TPSA 73.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC83253930 ZINC	0.688	224.3 Da LogP 0.61 TPSA 36.9	✓ Ro5	✓ Clean	`COCCOCCOCCOCCS`
ZINC83253936 ZINC	0.688	383.5 Da LogP -0.29 TPSA 99.9	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCN`
ZINC90556279 ZINC	0.688	295.4 Da LogP -0.33 TPSA 81.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCN`
ZINC90556280 ZINC	0.688	339.4 Da LogP -0.31 TPSA 90.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCN`
ZINC90556286 ZINC	0.688	312.4 Da LogP 0.65 TPSA 55.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCS`
ZINC90556287 ZINC	0.688	268.4 Da LogP 0.63 TPSA 46.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCS`
ZINC96503353 ZINC	0.688	471.6 Da LogP -0.26 TPSA 118.3	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCN`
ZINC104869865 ZINC	0.684	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O…`
ZINC12504289 ZINC	0.684	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC34541308 ZINC	0.684	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC35000839 ZINC	0.684	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC4284463 ZINC	0.684	250.2 Da LogP -1.82 TPSA 149.2	✓ Ro5	✓ Clean	`O=S(=O)(O)[C@H](O)CC[C@@H](O)S(=O)(=O)O`
ZINC4284464 ZINC	0.684	250.2 Da LogP -1.82 TPSA 149.2	✓ Ro5	✓ Clean	`O=S(=O)(O)[C@H](O)CC[C@H](O)S(=O)(=O)O`
ZINC4284466 ZINC	0.684	250.2 Da LogP -1.82 TPSA 149.2	✓ Ro5	✓ Clean	`O=S(=O)(O)[C@@H](O)CC[C@H](O)S(=O)(=O)O`
ZINC45284491 ZINC	0.684	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC80639694 ZINC	0.684	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC8215481 ZINC	0.684	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC104256315 ZINC	0.667	266.4 Da LogP 3.11 TPSA 74.6	✓ Ro5	✓ Clean	`CCCCCCCCCCC[C@@H](O)S(=O)(=O)O`
ZINC1598692 ZINC	0.667	266.4 Da LogP 3.11 TPSA 74.6	✓ Ro5	✓ Clean	`CCCCCCCCCCC[C@H](O)S(=O)(=O)O`
ZINC59681871 ZINC	0.667	322.5 Da LogP 4.67 TPSA 74.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCC[C@@H](O)S(=O)(=O)O`
ZINC59681874 ZINC	0.667	322.5 Da LogP 4.67 TPSA 74.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCC[C@H](O)S(=O)(=O)O`
ZINC113456917 ZINC	0.647	220.3 Da LogP 1.48 TPSA 36.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCOC`
ZINC146934560 ZINC	0.647	397.5 Da LogP -0.03 TPSA 85.9	✓ Ro5	✓ Clean	`COCCOCCOCCOCCNCCOCCOCCOCCOC`
ZINC218810670 ZINC	0.647	308.4 Da LogP 1.52 TPSA 55.4	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCOCCOCCOC`
ZINC33506597 ZINC	0.647	309.4 Da LogP -0.06 TPSA 67.4	✓ Ro5	✓ Clean	`COCCOCCOCCNCCOCCOCCOC`
ZINC34303570 ZINC	0.647	264.4 Da LogP 1.50 TPSA 46.2	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCOCCOC`
ZINC3860567 ZINC	0.647	323.4 Da LogP 0.28 TPSA 58.6	✓ Ro5	✓ Clean	`COCCOCCN(CCOCCOC)CCOCCOC`

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.

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A0A0H3GWP6