Protein profile

KP13_01630

tRNA (cmo5U34)-methyltransferase

Genome: KpKP13

Gene: cmoA AHE43848.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GS19

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Amino acids 247

Annotations 6

Features 15

PDB binders 3

Druggability 0.889

Overview

Basic information about this protein and its source genome.

Accession: KP13_01630
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: cmoA AHE43848.1
Status: annotated
Amino acids: 247
Structure source: AlphaFold + ColabFold

2.1.3.-

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.

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: Cytoplasmic
ColabFold pLDDT: 92.43

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 0.889

Structure A0A0H3GS19

Pocket Pocket 3

P2Rank 0.964

Structure A0A0H3GS19

Pocket Pocket 1

ColabFold model

FPocket 0.984 · Pocket 1

P2Rank 0.976 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 151 / 4744 genomes with a hit

Normalized 0.032

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

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 Features

Domain/signature hits 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; predicted models typically cover the full protein.

Loading 3D structure...

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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_A0A0H3GS19	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_01630	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
3				0.889

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	36.25	0.955
2	2.57	0.073
3	1.3	0.014

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				0.984

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	42.66	0.968
2	2.21	0.054
3	1.33	0.015

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

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
ASE	4A6E	P46597	218.3 Da LogP 1.55 TPSA 65.1	✓ Ro5	✓ Clean	`CC(=O)NCCc1c[nH]c2c1cc(cc2)O`
GEK	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	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	1.000	218.3 Da LogP 1.55 TPSA 65.1	✓ Ro5	✓ Clean	`CC(=O)NCCc1c[nH]c2ccc(O)cc12`
ZINC22048030	0.738	217.3 Da LogP 1.43 TPSA 70.9	✓ Ro5	✓ Clean	`CC(=O)NCCc1c[nH]c2ccc(N)cc12`
ZINC488387	0.738	236.7 Da LogP 2.50 TPSA 44.9	✓ Ro5	✓ Clean	`CC(=O)NCCc1c[nH]c2ccc(Cl)cc12`
ZINC77351	0.738	220.2 Da LogP 1.99 TPSA 44.9	✓ Ro5	✓ Clean	`CC(=O)NCCc1c[nH]c2ccc(F)cc12`
ZINC38778809	0.711	276.3 Da LogP 2.94 TPSA 74.3	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)NCCc1c[nH]c2ccc(O)cc12`
ZINC2557966	0.705	260.3 Da LogP 1.77 TPSA 71.2	✓ Ro5	✓ Clean	`CC(=O)NCCc1c[nH]c2ccc(OC(C)=O)cc12`
ZINC57060	0.705	232.3 Da LogP 1.86 TPSA 54.1	✓ Ro5	✓ Clean	`COc1ccc2[nH]cc(CCNC(C)=O)c2c1`
ZINC174849	0.683	202.3 Da LogP 1.85 TPSA 44.9	✓ Ro5	✓ Clean	`CC(=O)NCCc1c[nH]c2ccccc12`
ZINC488399	0.674	247.3 Da LogP 1.75 TPSA 88.0	✓ Ro5	✓ Clean	`CC(=O)NCCc1c[nH]c2ccc([N+](=O)[O-])cc12`
ZINC2567732	0.660	275.3 Da LogP 2.02 TPSA 83.2	✓ Ro5	✓ Clean	`COC(=O)Nc1ccc2[nH]cc(CCNC(C)=O)c2c1`
ZINC1587152	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	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	0.646	276.3 Da LogP 1.31 TPSA 91.4	✓ Ro5	✓ Clean	`CC(=O)NCCc1c[nH]c2ccc(OCC(=O)O)cc12`
ZINC5553933	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	0.644	295.2 Da LogP 3.00 TPSA 44.9	✓ Ro5	✓ Clean	`CC(=O)NCCCc1c[nH]c2ccc(Br)cc12`
ZINC2026768	0.644	230.3 Da LogP 2.55 TPSA 44.9	✓ Ro5	✓ Clean	`CC(=O)NCCCc1c[nH]c2ccc(C)cc12`
ZINC2496147	0.640	308.4 Da LogP 3.43 TPSA 54.1	✓ Ro5	✓ Clean	`CC(=O)NCCc1c[nH]c2ccc(OCc3ccccc3)cc12`
ZINC1771583	0.630	250.7 Da LogP 2.89 TPSA 44.9	✓ Ro5	✓ Clean	`CC(=O)NCCCc1c[nH]c2ccc(Cl)cc12`
ZINC95628425	0.620	346.4 Da LogP 3.70 TPSA 85.4	✓ Ro5	✓ Clean	`O=C(NCCc1c[nH]c2ccc(O)cc12)c1ccc2ccccc2c1O`
ZINC57344	0.617	248.3 Da LogP 1.56 TPSA 74.3	✓ Ro5	✓ Clean	`COc1cc2c(CCNC(C)=O)c[nH]c2cc1O`
ZINC95936163	0.605	205.2 Da LogP 1.59 TPSA 62.3	✓ Ro5	✓ Clean	`COC(=O)Cc1c[nH]c2ccc(O)cc12`
ZINC2325785154	0.604	344.5 Da LogP 2.64 TPSA 89.2	✓ Ro5	✓ Clean	`CNC1(CNC(=O)NCCc2c[nH]c3ccc(O)cc23)CCCCC1`
ZINC12371977	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	0.595	219.3 Da LogP 2.12 TPSA 36.0	✓ Ro5	✓ Clean	`C[N+](C)(C)CCc1c[nH]c2ccc(O)cc12`
ZINC13738655	0.591	229.3 Da LogP 2.22 TPSA 49.3	✓ Ro5	✓ Clean	`CC(=O)NCCc1cccc2ccc(O)cc12`
ZINC197798973	0.591	245.3 Da LogP 1.93 TPSA 69.6	✓ Ro5	✓ Clean	`CC(=O)NCCc1cc(O)cc2ccc(O)cc12`
ZINC1587150	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	0.589	352.4 Da LogP 2.96 TPSA 94.6	✓ Ro5	✓ Clean	`COc1cc(C=CC(=O)NCCc2c[nH]c3ccc(O)cc23)ccc1O`
ZINC2438607	0.587	244.3 Da LogP 2.79 TPSA 44.9	✓ Ro5	✓ Clean	`Cc1ccc2[nH]cc(CCNC(=O)C(C)C)c2c1`
ZINC1070	0.581	204.3 Da LogP 1.98 TPSA 39.3	✓ Ro5	✓ Clean	`CN(C)CCc1c[nH]c2ccc(O)cc12`
ZINC1759385	0.580	261.3 Da LogP 2.14 TPSA 88.0	✓ Ro5	✓ Clean	`CC(=O)NCCCc1c[nH]c2ccc([N+](=O)[O-])cc12`
ZINC20081854	0.574	306.4 Da LogP 3.69 TPSA 44.9	✓ Ro5	✓ Clean	`Cc1ccc(CC(=O)NCCc2c[nH]c3ccc(C)cc23)cc1`
ZINC1507228	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	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	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.