Protein target profile

KP13_01706

Porphobilinogen deaminase

Genome: KpKP13 Gene: hemC AHE46988.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GKD9

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Length 313

Pocket druggability 0.52

Direct ligand evidence 0 7 total records

Functional annotation 1 EC 5 GO

Target summary

Promising target candidate with multiple supporting evidence streams.

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

Main supporting evidence

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Moderate predicted binding pocket FPocket selected-pocket score 0.52. This supports review but is not experimental validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.94. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

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: Hit
Human identity (%): 47.312 Lower values reduce human off-target concern.
Human E-value: 4.91e-50
Gut microbiome similarity: 8.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 83.974 Higher values support similarity to known essential genes.
DEG E-value: 0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 93.2 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.52

Structure A0A0H3GKD9

Pocket Pocket 6

P2Rank 0.942

Structure A0A0H3GKD9

Pocket Pocket 1

ColabFold model

FPocket 0.832 · Pocket 7

P2Rank 0.943 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 394 / 4744 genomes with a hit

Prevalence 8.3%

Cross-references

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

Sequence

UniProt A0A0H3GKD9

Sequence

Primary amino-acid sequence viewer.

MLDKVLKIATRQSPLALWQAQYVKARLEQAHPGLKVELVPMVTRGDVILDTPLAKVGGKGLFVKELELAMLEGRADIAVHSMKDVPVEFPEGLGLVTICERDDPRDAFVSNRYASIDELPAGSVVGTSSLRRQCQLAATRPDLAIRSLRGNVGTRLSKLDNGEYDAIILAAAGLKRLQLEARIRQPLSPEQSLPAVGQGAVGIECRLDDAWTRGLLAPLNHTETAVRVRAERAMNTRLEGGCQVPIGSYAELKDGELWLRALVGAPDGSQLVRGERRGPAEQAEALGISLAEELLDNGAREILAAVYDGEAPR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

2.5.1.61

Gene Ontology (GO)

GO:0004418 Catalysis of the reaction: H2O + 4 porphobilinogen = hydroxymethylbilane + 4 NH4.
GO:0033014 The chemical reactions and pathways leading to the formation of tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.
GO:0018160 The covalent binding of a pyrromethane (dipyrrin) cofactor to protein via the sulfur atom of cysteine forming dipyrrolylmethanemethyl-L-cysteine.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0006782 The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

35 records

Show feature table

Start	End	DB	Term	Name
1	311	PIRSF	PIRSF001438	PBGD
1	311	InterPro	IPR000860	Porphobilinogen deaminase
5	297	Hamap	MF_00260	Porphobilinogen deaminase [hemC].
5	297	InterPro	IPR000860	Porphobilinogen deaminase
6	209	Gene3D	G3DSA:3.40.190.10	-
103	202	Gene3D	G3DSA:3.40.190.10	-
221	309	Gene3D	G3DSA:3.30.160.40	-
221	309	InterPro	IPR036803	Porphobilinogen deaminase, C-terminal domain superfamily
6	212	Pfam	PF01379	Porphobilinogen deaminase, dipyromethane cofactor binding domain
6	212	InterPro	IPR022417	Porphobilinogen deaminase, N-terminal
221	310	FunFam	G3DSA:3.30.160.40:FF:000002	Porphobilinogen deaminase
5	219	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II
45	65	PRINTS	PR00151	Porphobilinogen deaminase signature
45	65	InterPro	IPR000860	Porphobilinogen deaminase
230	247	PRINTS	PR00151	Porphobilinogen deaminase signature
230	247	InterPro	IPR000860	Porphobilinogen deaminase
76	95	PRINTS	PR00151	Porphobilinogen deaminase signature
76	95	InterPro	IPR000860	Porphobilinogen deaminase
124	141	PRINTS	PR00151	Porphobilinogen deaminase signature
124	141	InterPro	IPR000860	Porphobilinogen deaminase
143	160	PRINTS	PR00151	Porphobilinogen deaminase signature
143	160	InterPro	IPR000860	Porphobilinogen deaminase
6	103	FunFam	G3DSA:3.40.190.10:FF:000004	Porphobilinogen deaminase
226	295	Pfam	PF03900	Porphobilinogen deaminase, C-terminal domain
226	295	InterPro	IPR022418	Porphobilinogen deaminase, C-terminal
220	308	SUPERFAMILY	SSF54782	Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain
220	308	InterPro	IPR036803	Porphobilinogen deaminase, C-terminal domain superfamily
104	202	FunFam	G3DSA:3.40.190.10:FF:000005	Porphobilinogen deaminase
6	278	CDD	cd13646	PBP2_EcHMBS_like
231	247	ProSitePatterns	PS00533	Porphobilinogen deaminase cofactor-binding site.
231	247	InterPro	IPR022419	Porphobilinogen deaminase, dipyrromethane cofactor binding site
6	297	NCBIfam	TIGR00212	hydroxymethylbilane synthase
6	297	InterPro	IPR000860	Porphobilinogen deaminase
4	306	PANTHER	PTHR11557	PORPHOBILINOGEN DEAMINASE
4	306	InterPro	IPR000860	Porphobilinogen deaminase

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 · FPocket

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

Site 1 FPocket #6

0.52

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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1

0.942

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Surrounding area

Binding pockets · FPocket

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

Site 1 FPocket #7

0.832

Likely same site as P2Rank 2 6.3 Å 6 shared residues 60% of smaller site

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Surrounding area

Site 2 FPocket #2

0.422

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Surrounding area

Site 3 FPocket #14

0.385

Likely same site as P2Rank 2 7.9 Å 3 shared residues 38% of smaller site

Show in viewer

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_A0A0H3GKD9	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_01706	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.

7 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 6 records from similar proteins

Structural ligands 6 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 1 similarity-based ZINC candidates

Best available ligand signal

18W PDB via homolog 434.4 Da · LogP 1.07 · TPSA 194.1 Open detail RCSB PDB

29P PDB via homolog Detail RCSB PDB

7J8 PDB via homolog Detail RCSB PDB

AWQ PDB via homolog Detail RCSB PDB

DPM 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
18W RCSB PDB	4HTG	Q43316	434.4 Da LogP 1.07 TPSA 194.1	1 viol.	✓ Clean	`Cc1c(c(c([nH]1)/C=C\2/C(=C(C(=O)N2)CCC(=O)O)CC(…`
29P RCSB PDB	4MLQ	Q8GCA8	436.4 Da LogP 0.64 TPSA 194.1	1 viol.	✓ Clean	`Cc1c(c(c([nH]1)C[C@H]2C(=C(C(=O)N2)CCC(=O)O)CC(…`
7J8 RCSB PDB	5M6R	P08397	838.8 Da LogP 2.66 TPSA 361.6	2 viol.	✓ Clean	`Cc1c(c(c([nH]1)Cc2c(c(c([nH]2)Cc3c(c(c([nH]3)Cc…`
AWQ RCSB PDB	5OV6	Q8GCA8	225.2 Da LogP 1.28 TPSA 90.4	✓ Ro5	✓ Clean	`Cc1c(c(c([nH]1)C)CC(=O)O)CCC(=O)O`
DPM RCSB PDB	1AH5	P06983	420.4 Da LogP 1.53 TPSA 180.8	1 viol.	✓ Clean	`Cc1c(c(c([nH]1)Cc2c(c(c[nH]2)CCC(=O)O)CC(=O)O)C…`
FWL RCSB PDB	7CCY	P08397	352.1 Da LogP 0.72 TPSA 116.4	✓ Ro5	✓ Clean	`C(CC(=O)O)c1c(c([nH]c1I)CN)CC(=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
ZINC56609 ZINC	0.581	226.2 Da LogP 0.12 TPSA 116.4	✓ Ro5	✓ Clean	`NCc1[nH]cc(CCC(=O)O)c1CC(=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.