KpKP13 Protein target profile

tRNA (cmo5U34)-methyltransferase

Accession: KP13_01630

Gene: cmoA AHE43848.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GS19

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Length 247

Pocket druggability (P2Rank · AlphaFold DB model) 0.964

Direct ligand evidence 0 53 total records

Functional annotation 1 EC 5 GO

Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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

Main supporting evidence

Independent pocket support: P2Rank + FPocket Both predictors report a high-scoring binding site (P2Rank 0.96, FPocket 0.89). Use the 3D pocket comparison to verify whether they identify the same site. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.89. This is a computational pocket signal, not binding validation. 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: No hit
Gut microbiome similarity: 3.2% 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: 92.43 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) 0.964

Structure A0A0H3GS19

Pocket Pocket 1

Druggability (FPocket) 0.889

Structure A0A0H3GS19

Pocket Pocket 3

ColabFold model

P2Rank 0.976 · Pocket 1

FPocket 0.984 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 151 / 4744 genomes with a hit

Prevalence 3.2%

Cross-references

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

Sequence

UniProt A0A0H3GS19

Sequence

Primary amino-acid sequence viewer.

MSHRDTLFSAPIASLGDWTFDERVAEVFPDMIQRSVPGYSNIISMIGMLAERFVQPNTQVYDLGCSLGAATLSVRRNISHPGCRIIAIDNSPAMVERCRRHIDAYKAPTPVEVIEGDIRDVTIENASLVILNFTIQFLEPGDRQAILNKVYQGLNPGGALVLSEKFSFEDAHVGELLFNMHHDFKRANGYSELEISQKRSMLENVMLTDSVETHKARLRQAGFEHAELWFQCFNFGSLVAVKAGEQA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Subcellular localization

Localization: Cytoplasmic

Enzyme Commission (EC)

2.1.3.-

Gene Ontology (GO)

GO:0002098 The process in which a uridine at position 34 of a tRNA is post-transcriptionally modified. The wobble nucleoside of the tRNA sequence (position 34) corresponds to the first position of the anticodon.
GO:0016743 Catalysis of the transfer of a carboxyl- or carbamoyl group from one compound (donor) to another (acceptor).
GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
GO:1904047 Binding to S-adenosyl-L-methionine.
GO:0032259 The process in which a methyl group is covalently attached to a molecule.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

15 records

Show feature table

Start	End	DB	Term	Name
18	247	FunFam	G3DSA:3.40.50.150:FF:000030	Carboxy-S-adenosyl-L-methionine synthase
20	242	SUPERFAMILY	SSF53335	S-adenosyl-L-methionine-dependent methyltransferases
20	242	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
60	158	Pfam	PF13649	Methyltransferase domain
60	158	InterPro	IPR041698	Methyltransferase domain 25
18	247	Gene3D	G3DSA:3.40.50.150	Vaccinia Virus protein VP39
18	247	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
1	243	PIRSF	PIRSF006325	Mtase_YecO
1	243	InterPro	IPR005271	Carboxy-S-adenosyl-L-methionine synthase
4	242	NCBIfam	TIGR00740	carboxy-S-adenosyl-L-methionine synthase CmoA
4	242	InterPro	IPR005271	Carboxy-S-adenosyl-L-methionine synthase
60	163	CDD	cd02440	AdoMet_MTases
3	242	Hamap	MF_01589	Carboxy-S-adenosyl-L-methionine synthase [cmoA].
3	242	InterPro	IPR005271	Carboxy-S-adenosyl-L-methionine synthase
5	232	PANTHER	PTHR43861	TRANS-ACONITATE 2-METHYLTRANSFERASE-RELATED

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

0.964

Likely same site as FPocket 3 1.5 Å 37 shared residues 97% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.135

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Surrounding area

Pocket 3 P2Rank #3

0.019

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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 #3

0.889 Unusual size

Likely same site as P2Rank 1 1.5 Å 37 shared residues 97% of smaller site

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Surrounding area

Residue sets

UniProt: Binding site:117-118

UniProt: Binding site:132-132

UniProt: Binding site:199-199

UniProt: Binding site:39-39

UniProt: Binding site:64-66

UniProt: Binding site:89-90

Binding pockets · P2Rank

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

Pocket 1 P2Rank #1

0.976

Likely same site as FPocket 1 6.7 Å 28 shared residues 93% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.086

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Surrounding area

Pocket 3 P2Rank #3

0.016

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Surrounding area

Pocket 4 P2Rank #4

0.001

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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_A0A0H3GS19	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_01630	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.

53 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 3 records from similar proteins

Structural ligands 3 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

ASE PDB via homolog 218.3 Da · LogP 1.55 · TPSA 65.1 Open detail RCSB PDB

GEK PDB via homolog Detail RCSB PDB

SAI PDB via homolog Detail RCSB PDB

ZINC66104 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

ZINC22048030 ZINC proposed compound · Tanimoto 0.738 Detail ZINC

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
ASE RCSB PDB	4A6E	P46597	218.3 Da LogP 1.55 TPSA 65.1	✓ Ro5	✓ Clean	`CC(=O)NCCc1c[nH]c2c1cc(cc2)O`
GEK RCSB PDB	4GEK	C3T5M2	442.5 Da LogP -5.85 TPSA 227.2	1 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
SAI RCSB PDB	1IM8	P43985	431.3 Da LogP -1.63 TPSA 182.6	✓ Ro5	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`

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
ZINC66104 ZINC	1.000	218.3 Da LogP 1.55 TPSA 65.1	✓ Ro5	✓ Clean	`CC(=O)NCCc1c[nH]c2ccc(O)cc12`
ZINC22048030 ZINC	0.738	217.3 Da LogP 1.43 TPSA 70.9	✓ Ro5	✓ Clean	`CC(=O)NCCc1c[nH]c2ccc(N)cc12`
ZINC488387 ZINC	0.738	236.7 Da LogP 2.50 TPSA 44.9	✓ Ro5	✓ Clean	`CC(=O)NCCc1c[nH]c2ccc(Cl)cc12`
ZINC77351 ZINC	0.738	220.2 Da LogP 1.99 TPSA 44.9	✓ Ro5	✓ Clean	`CC(=O)NCCc1c[nH]c2ccc(F)cc12`
ZINC38778809 ZINC	0.711	276.3 Da LogP 2.94 TPSA 74.3	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)NCCc1c[nH]c2ccc(O)cc12`
ZINC2557966 ZINC	0.705	260.3 Da LogP 1.77 TPSA 71.2	✓ Ro5	✓ Clean	`CC(=O)NCCc1c[nH]c2ccc(OC(C)=O)cc12`
ZINC57060 ZINC	0.705	232.3 Da LogP 1.86 TPSA 54.1	✓ Ro5	✓ Clean	`COc1ccc2[nH]cc(CCNC(C)=O)c2c1`
ZINC174849 ZINC	0.683	202.3 Da LogP 1.85 TPSA 44.9	✓ Ro5	✓ Clean	`CC(=O)NCCc1c[nH]c2ccccc12`
ZINC488399 ZINC	0.674	247.3 Da LogP 1.75 TPSA 88.0	✓ Ro5	✓ Clean	`CC(=O)NCCc1c[nH]c2ccc([N+](=O)[O-])cc12`
ZINC2567732 ZINC	0.660	275.3 Da LogP 2.02 TPSA 83.2	✓ Ro5	✓ Clean	`COC(=O)Nc1ccc2[nH]cc(CCNC(C)=O)c2c1`
ZINC1587152 ZINC	0.646	322.4 Da LogP 2.95 TPSA 85.4	✓ Ro5	✓ Clean	`O=C(/C=C/c1ccc(O)cc1)NCCc1c[nH]c2ccc(O)cc12`
ZINC1875251665 ZINC	0.646	322.4 Da LogP 2.95 TPSA 85.4	✓ Ro5	✓ Clean	`O=C(C=Cc1ccc(O)cc1)NCCc1c[nH]c2ccc(O)cc12`
ZINC468353 ZINC	0.646	276.3 Da LogP 1.31 TPSA 91.4	✓ Ro5	✓ Clean	`CC(=O)NCCc1c[nH]c2ccc(OCC(=O)O)cc12`
ZINC5553933 ZINC	0.646	322.4 Da LogP 2.95 TPSA 85.4	✓ Ro5	✓ Clean	`O=C(/C=C\c1ccc(O)cc1)NCCc1c[nH]c2ccc(O)cc12`
ZINC1828812 ZINC	0.644	295.2 Da LogP 3.00 TPSA 44.9	✓ Ro5	✓ Clean	`CC(=O)NCCCc1c[nH]c2ccc(Br)cc12`
ZINC2026768 ZINC	0.644	230.3 Da LogP 2.55 TPSA 44.9	✓ Ro5	✓ Clean	`CC(=O)NCCCc1c[nH]c2ccc(C)cc12`
ZINC2496147 ZINC	0.640	308.4 Da LogP 3.43 TPSA 54.1	✓ Ro5	✓ Clean	`CC(=O)NCCc1c[nH]c2ccc(OCc3ccccc3)cc12`
ZINC1771583 ZINC	0.630	250.7 Da LogP 2.89 TPSA 44.9	✓ Ro5	✓ Clean	`CC(=O)NCCCc1c[nH]c2ccc(Cl)cc12`
ZINC95628425 ZINC	0.620	346.4 Da LogP 3.70 TPSA 85.4	✓ Ro5	✓ Clean	`O=C(NCCc1c[nH]c2ccc(O)cc12)c1ccc2ccccc2c1O`
ZINC57344 ZINC	0.617	248.3 Da LogP 1.56 TPSA 74.3	✓ Ro5	✓ Clean	`COc1cc2c(CCNC(C)=O)c[nH]c2cc1O`
ZINC95936163 ZINC	0.605	205.2 Da LogP 1.59 TPSA 62.3	✓ Ro5	✓ Clean	`COC(=O)Cc1c[nH]c2ccc(O)cc12`
ZINC2325785154 ZINC	0.604	344.5 Da LogP 2.64 TPSA 89.2	✓ Ro5	✓ Clean	`CNC1(CNC(=O)NCCc2c[nH]c3ccc(O)cc23)CCCCC1`
ZINC12371977 ZINC	0.600	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c…`
ZINC12371978 ZINC	0.600	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c(…`
ZINC13522357 ZINC	0.600	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@@+](CC[C@@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3…`
ZINC13522362 ZINC	0.600	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c…`
ZINC139339614 ZINC	0.600	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@@+](CC[C@H](N)C(=O)O)C[C@@H]1O[C@H](n2cnc3c…`
ZINC254297245 ZINC	0.600	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@H](N)C(=O)O)C[C@@H]1O[C@H](n2cnc3c(…`
ZINC254297254 ZINC	0.600	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@H](N)C(=O)O)C[C@@H]1O[C@H](n2cnc3c(…`
ZINC254297257 ZINC	0.600	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@H](N)C(=O)O)C[C@@H]1O[C@H](n2cnc3c(…`
ZINC33821030 ZINC	0.600	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c…`
ZINC33821031 ZINC	0.600	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c(…`
ZINC4214738 ZINC	0.600	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c…`
ZINC4228231 ZINC	0.600	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c(…`
ZINC71755544 ZINC	0.600	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@@H](N)C(=O)O)C[C@@H]1O[C@H](n2cnc3c…`
ZINC71755557 ZINC	0.600	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@@+](CC[C@@H](N)C(=O)O)C[C@@H]1O[C@H](n2cnc3…`
ZINC95644663 ZINC	0.600	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c…`
ZINC95644664 ZINC	0.600	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c(…`
ZINC2572276 ZINC	0.595	219.3 Da LogP 2.12 TPSA 36.0	✓ Ro5	✓ Clean	`C[N+](C)(C)CCc1c[nH]c2ccc(O)cc12`
ZINC13738655 ZINC	0.591	229.3 Da LogP 2.22 TPSA 49.3	✓ Ro5	✓ Clean	`CC(=O)NCCc1cccc2ccc(O)cc12`
ZINC197798973 ZINC	0.591	245.3 Da LogP 1.93 TPSA 69.6	✓ Ro5	✓ Clean	`CC(=O)NCCc1cc(O)cc2ccc(O)cc12`
ZINC1587150 ZINC	0.589	352.4 Da LogP 2.96 TPSA 94.6	✓ Ro5	✓ Clean	`COc1cc(/C=C/C(=O)NCCc2c[nH]c3ccc(O)cc23)ccc1O`
ZINC2297332751 ZINC	0.589	352.4 Da LogP 2.96 TPSA 94.6	✓ Ro5	✓ Clean	`COc1cc(C=CC(=O)NCCc2c[nH]c3ccc(O)cc23)ccc1O`
ZINC2438607 ZINC	0.587	244.3 Da LogP 2.79 TPSA 44.9	✓ Ro5	✓ Clean	`Cc1ccc2[nH]cc(CCNC(=O)C(C)C)c2c1`
ZINC1070 ZINC	0.581	204.3 Da LogP 1.98 TPSA 39.3	✓ Ro5	✓ Clean	`CN(C)CCc1c[nH]c2ccc(O)cc12`
ZINC1759385 ZINC	0.580	261.3 Da LogP 2.14 TPSA 88.0	✓ Ro5	✓ Clean	`CC(=O)NCCCc1c[nH]c2ccc([N+](=O)[O-])cc12`
ZINC20081854 ZINC	0.574	306.4 Da LogP 3.69 TPSA 44.9	✓ Ro5	✓ Clean	`Cc1ccc(CC(=O)NCCc2c[nH]c3ccc(C)cc23)cc1`
ZINC1507228 ZINC	0.574	301.3 Da LogP 1.06 TPSA 94.2	✓ Ro5	✓ Clean	`O=C1NCCC[C@@H]1C(=O)NCCc1c[nH]c2ccc(O)cc12`
ZINC1507230 ZINC	0.574	301.3 Da LogP 1.06 TPSA 94.2	✓ Ro5	✓ Clean	`O=C1NCCC[C@H]1C(=O)NCCc1c[nH]c2ccc(O)cc12`
ZINC57237 ZINC	0.571	266.7 Da LogP 2.51 TPSA 54.1	✓ Ro5	✓ Clean	`COc1cc2c(CCNC(C)=O)c[nH]c2cc1Cl`

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.