KpKP13 Protein target profile

putative hydrolase

Accession: KP13_03348

Gene: AHE45727.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GJX7

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Length 241

Pocket druggability (P2Rank · AlphaFold DB model) 0.817

Direct ligand evidence 0 33 total records

Functional annotation 0 EC 1 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

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.82. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 6 structural and 2 bioactivity records.

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 (%): 36.111 Lower values reduce human off-target concern.
Human E-value: 1.51e-36
Gut microbiome similarity: 1.6% 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: 96.67 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) 0.817

Structure A0A0H3GJX7

Pocket Pocket 1

Druggability (FPocket) 0.327

Structure A0A0H3GJX7

Pocket Pocket 1

ColabFold model

P2Rank 0.767 · Pocket 1

FPocket 0.56 · Pocket 13

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 77 / 4744 genomes with a hit

Prevalence 1.6%

Sequence

Primary amino-acid sequence viewer.

MAMMQQAEREGAALLVLPEALLARDDNDPDLSVKSAQPLDGAFLQPLLAESRRNSLTTVLTLHVPSGEGRATNTLVVLREGAVIAHYHKLHLYDAFAMQESRRVDPGQQIPPVIEVAGLRVGLMTCYDLRFPELALSLALNGAQLLVLPAAWVKGPQKEYHWATLLAARALDTTCYIVAAGECGTRNIGLSRIVDPLGTTLAGAGSEPQLIFADLSADDLARVRERLPVLRNRRFAPPQLL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Subcellular localization

Localization: Cytoplasmic

Gene Ontology (GO)

GO:0006807 OBSOLETE. The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records

Show feature table

Start	End	DB	Term	Name
1	236	Gene3D	G3DSA:3.60.110.10	-
1	236	InterPro	IPR036526	Carbon-nitrogen hydrolase superfamily
3	235	PANTHER	PTHR23088	NITRILASE-RELATED
11	18	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
122	142	ProSitePatterns	PS01227	Uncharacterized protein family UPF0012 signature.
122	142	InterPro	IPR001110	Uncharacterised protein family UPF0012, conserved site
1	23	Phobius	SIGNAL_PEPTIDE	Signal peptide region
1	10	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
1	217	ProSiteProfiles	PS50263	Carbon-nitrogen hydrolase domain profile.
1	217	InterPro	IPR003010	Carbon-nitrogen hydrolase
4	234	CDD	cd07581	nitrilase_3
24	241	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
19	23	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
2	240	NCBIfam	NF033621	deaminated glutathione amidase
2	236	SUPERFAMILY	SSF56317	Carbon-nitrogen hydrolase
2	236	InterPro	IPR036526	Carbon-nitrogen hydrolase superfamily
2	224	Pfam	PF00795	Carbon-nitrogen hydrolase
2	224	InterPro	IPR003010	Carbon-nitrogen hydrolase

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

0.817

Likely same site as FPocket 1 1.3 Å 23 shared residues 96% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.013

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Surrounding area

Pocket 3 P2Rank #3

0.008

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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 #1

0.327 Unusual size

Likely same site as P2Rank 1 1.3 Å 23 shared residues 96% of smaller site

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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

0.767

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Surrounding area

Pocket 2 P2Rank #2

0.108

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Surrounding area

Pocket 3 P2Rank #3

0.09

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Surrounding area

Pocket 4 P2Rank #4

0.077

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Surrounding area

Pocket 5 P2Rank #5

0.017

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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_A0A0H3GJX7	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_03348	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.

33 records

Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records

Transferred evidence 8 records from similar proteins

Structural ligands 6 0 loaded crystals

Measured bioactivity 2 direct and transferred ChEMBL records

Proposed compounds 25 similarity-based ZINC candidates

Best available ligand signal

AKG PDB via homolog 146.1 Da · LogP -0.50 · TPSA 91.7 Open detail RCSB PDB

CAC PDB via homolog Detail RCSB PDB

EMC PDB via homolog Detail RCSB PDB

KGT PDB via homolog Detail RCSB PDB

OAA 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
AKG RCSB PDB	4HG3	P47016	146.1 Da LogP -0.50 TPSA 91.7	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)C(=O)O`
CAC RCSB PDB	4H5U	P47016	137.0 Da LogP -0.52 TPSA 40.1	✓ Ro5	✓ Clean	`C[As](=O)(C)[O-]`
EMC RCSB PDB	1EMS	O76463	229.7 Da LogP 0.97 TPSA 0.0	✓ Ro5	✓ Clean	`CC[Hg+]`
KGT RCSB PDB	4HGD	P47016	306.3 Da LogP -1.96 TPSA 149.9	✓ Ro5	✓ Clean	`C(CC(=O)N[C@@H](CS)C(=O)NCC(=O)O)C(=O)C(=O)O`
OAA RCSB PDB	4HG5	P47016	131.1 Da LogP -2.22 TPSA 94.5	✓ Ro5	✓ Clean	`C(C(=O)C(=O)O)C(=O)[O-]`
P6W RCSB PDB	6YPA	O58376	130.1 Da LogP -0.87 TPSA 86.2	✓ Ro5	✓ Clean	`C(CC(=O)N)CC(=O)N`

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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
DWT ChEMBL	Q9NQR4	8.58 ~2.6 nM	503.5 Da LogP 5.75 TPSA 97.6	2 viol.	✓ Clean	`Cc1ccc(cc1Nc2c3cn(nc3nc(n2)c4cccnc4)C)C(=O)Nc5c…`
CHEMBL4129274 ChEMBL	Q86X76	—	851.5 Da LogP 4.76 TPSA 183.3	3 viol.	Alert	`C=CC(=O)Nc1ccccc1Nc1nc(Nc2ccc(N3CCN(CCOCCOCCOCC…`

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
ZINC116475206 ZINC	0.769	284.4 Da LogP 3.42 TPSA 86.2	✓ Ro5	✓ Clean	`NC(=O)CCCCCCCCCCCCCCC(N)=O`
ZINC1587906 ZINC	0.769	200.3 Da LogP 1.08 TPSA 86.2	✓ Ro5	✓ Clean	`NC(=O)CCCCCCCCC(N)=O`
ZINC71771467 ZINC	0.769	256.4 Da LogP 2.64 TPSA 86.2	✓ Ro5	✓ Clean	`NC(=O)CCCCCCCCCCCCC(N)=O`
ZINC4899752 ZINC	0.649	235.3 Da LogP -2.44 TPSA 121.5	✓ Ro5	✓ Clean	`NCC(=O)N[C@@H](CS)C(=O)NCC(=O)O`
ZINC13545198 ZINC	0.639	220.2 Da LogP -1.38 TPSA 95.5	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CS)C(=O)NCC(=O)O`
ZINC3830891 ZINC	0.634	307.3 Da LogP -2.21 TPSA 158.8	1 viol.	✓ Clean	`N[C@@H](CCC(=O)N[C@@H](CS)C(=O)NCC(=O)O)C(=O)O`
ZINC3830892 ZINC	0.634	307.3 Da LogP -2.21 TPSA 158.8	1 viol.	✓ Clean	`N[C@@H](CCC(=O)N[C@H](CS)C(=O)NCC(=O)O)C(=O)O`
ZINC3830893 ZINC	0.634	307.3 Da LogP -2.21 TPSA 158.8	1 viol.	✓ Clean	`N[C@H](CCC(=O)N[C@@H](CS)C(=O)NCC(=O)O)C(=O)O`
ZINC3830894 ZINC	0.634	307.3 Da LogP -2.21 TPSA 158.8	1 viol.	✓ Clean	`N[C@H](CCC(=O)N[C@H](CS)C(=O)NCC(=O)O)C(=O)O`
ZINC13549503 ZINC	0.591	321.4 Da LogP -2.12 TPSA 147.8	✓ Ro5	✓ Clean	`COC(=O)[C@@H](N)CCC(=O)N[C@@H](CS)C(=O)NCC(=O)O`
ZINC1693895 ZINC	0.556	227.4 Da LogP 4.17 TPSA 43.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(N)=O`
ZINC2170606 ZINC	0.556	213.4 Da LogP 3.78 TPSA 43.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(N)=O`
ZINC44630074 ZINC	0.556	217.4 Da LogP 2.91 TPSA 43.1	✓ Ro5	✓ Clean	`NC(=O)CCCCCCCCCCS`
ZINC86040350 ZINC	0.556	241.4 Da LogP 4.56 TPSA 43.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCC(N)=O`
ZINC8689949 ZINC	0.556	255.4 Da LogP 4.95 TPSA 43.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(N)=O`
ZINC95910974 ZINC	0.556	287.5 Da LogP 4.86 TPSA 43.1	✓ Ro5	✓ Clean	`NC(=O)CCCCCCCCCCCCCCCS`
ZINC71842002 ZINC	0.552	445.6 Da LogP 2.04 TPSA 76.7	✓ Ro5	✓ Clean	`O=C(CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12)NCCCN1CC…`
ZINC220133900 ZINC	0.538	398.3 Da LogP 3.77 TPSA 85.1	✓ Ro5	✓ Clean	`Cc1nc2nc(-c3cccnc3)nn2cc1C(=O)Nc1cccc(C(F)(F)F)…`
ZINC20148987 ZINC	0.532	414.4 Da LogP 4.50 TPSA 97.1	✓ Ro5	✓ Clean	`Cc1ccc(C(=O)Nc2cccc(C(F)(F)F)c2)cc1Nc1cncc(C(N)…`
ZINC914431236 ZINC	0.531	464.0 Da LogP 4.49 TPSA 85.4	✓ Ro5	Alert	`C=CC(=O)Nc1ccccc1Nc1nc(Nc2ccc(N3CCN(C)CC3)cc2)n…`
ZINC1640977 ZINC	0.529	230.3 Da LogP -2.09 TPSA 132.5	✓ Ro5	✓ Clean	`NC(=O)CCN(CCC(N)=O)CCC(N)=O`
ZINC9306398 ZINC	0.512	398.3 Da LogP 3.77 TPSA 85.1	✓ Ro5	✓ Clean	`Cc1c(C(=O)Nc2cccc(C(F)(F)F)c2)cnc2nc(-c3cccnc3)…`
ZINC5828410 ZINC	0.511	306.3 Da LogP -2.81 TPSA 164.6	1 viol.	✓ Clean	`NC(=O)CNC(=O)[C@H](CS)NC(=O)CC[C@H](N)C(=O)O`
ZINC5049572 ZINC	0.507	336.3 Da LogP 4.22 TPSA 58.2	✓ Ro5	✓ Clean	`CC(=O)Nc1cc(C(=O)Nc2cccc(C(F)(F)F)c2)ccc1C`
ZINC1688613 ZINC	0.500	263.2 Da LogP -1.02 TPSA 146.3	✓ Ro5	✓ Clean	`NC(=O)CCP(=O)(CCC(N)=O)CCC(N)=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.

Cross-references

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

Sequence

UniProt A0A0H3GJX7

Chemistry

ChEMBL DWT ChEMBL CHEMBL4129274