Protein profile

KP13_03364

Acireductone dioxygenase bifunctional protein

Genome: KpKP13

Gene: AHE45743.1 mtnD Structure source: AlphaFold + ColabFold UniProt A0A0H3GTU3

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Amino acids 180

Annotations 8

Features 12

PDB binders 4

Druggability 0.91

Overview

Basic information about this protein and its source genome.

Accession: KP13_03364
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE45743.1 mtnD
Status: annotated
Amino acids: 180
Structure source: AlphaFold + ColabFold

1.13.11.54 1.13.11.53

GO:0010309 Catalysis of the reaction: 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2 = 4-methylthio-2-oxobutanoate + formate + H+. GO:0016151 Binding to a nickel (Ni) cation. GO:0005506 Binding to an iron (Fe) ion. GO:0010308 Catalysis of the reaction: 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2 = 3-(methylthio)propanoate + CO + formate. GO:0019284 OBSOLETE. The chemical reactions and pathways resulting in the formation of L-methionine from S-adenosylmethionine. GO:0019509 OBSOLETE. The generation of L-methionine (2-amino-4-(methylthio)butanoic acid) from methylthioadenosine.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 34.667
Human E-value: 1.85e-07
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 92.22

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 0.91

Structure A0A0H3GTU3

Pocket Pocket 2

P2Rank 0.79

Structure A0A0H3GTU3

Pocket Pocket 1

ColabFold model

FPocket 0.528 · Pocket 1

P2Rank 0.546 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 81 / 4744 genomes with a hit

Normalized 0.017

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 6 GO

Enzyme Commission (EC)

Gene Ontology (GO)

GO:0010309 Catalysis of the reaction: 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2 = 4-methylthio-2-oxobutanoate + formate + H+.
GO:0016151 Binding to a nickel (Ni) cation.
GO:0005506 Binding to an iron (Fe) ion.
GO:0010308 Catalysis of the reaction: 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2 = 3-(methylthio)propanoate + CO + formate.
GO:0019284 OBSOLETE. The chemical reactions and pathways resulting in the formation of L-methionine from S-adenosylmethionine.
GO:0019509 OBSOLETE. The generation of L-methionine (2-amino-4-(methylthio)butanoic acid) from methylthioadenosine.

Sequence Features

Domain/signature hits from InterPro and related databases.

12 records

Show feature table

Start	End	DB	Term	Name
1	172	Hamap	MF_01682	Acireductone dioxygenase [mtnD].
1	172	InterPro	IPR023956	Acireductone dioxygenase ARD, bacteria
2	157	Gene3D	G3DSA:2.60.120.10	Jelly Rolls
2	157	InterPro	IPR014710	RmlC-like jelly roll fold
18	165	Pfam	PF03079	ARD/ARD' family
18	165	InterPro	IPR004313	Acireductone dioxygenase ARD family
11	170	PANTHER	PTHR23418	ACIREDUCTONE DIOXYGENASE
11	170	InterPro	IPR004313	Acireductone dioxygenase ARD family
27	165	CDD	cd02232	cupin_ARD
27	165	InterPro	IPR004313	Acireductone dioxygenase ARD family
4	178	SUPERFAMILY	SSF51182	RmlC-like cupins
4	178	InterPro	IPR011051	RmlC-like cupin domain superfamily

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_A0A0H3GTU3	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_03364	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
2				0.91

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				14.1	0.711

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				0.528

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				9.85	0.529

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.

54 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
69O	5I93	Q99JT9	116.1 Da LogP 0.44 TPSA 54.4	✓ Ro5	✓ Clean	`CCCC(=O)C(=O)O`
KMT	5I8Y	Q99JT9	148.2 Da LogP 0.39 TPSA 54.4	✓ Ro5	✓ Clean	`CSCCC(=O)C(=O)O`
LAC	5I8T	Q99JT9	90.1 Da LogP -0.55 TPSA 57.5	✓ Ro5	✓ Clean	`C[C@H](C(=O)O)O`
LEA	5I8S	Q99JT9	102.1 Da LogP 1.26 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCC(=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
ZINC1529498	0.778	200.3 Da LogP 3.99 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)O`
ZINC1530417	0.778	228.4 Da LogP 4.77 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)O`
ZINC1628119	0.778	214.3 Da LogP 4.38 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)O`
ZINC2113934081	0.750	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCCCCCC(=O)O`
ZINC2243668	0.750	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCC(=O)O`
ZINC2378799	0.750	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCC(=O)O`
ZINC33820423	0.750	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCCCC(=O)O`
ZINC2378801	0.700	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCC(=O)O`
ZINC138457918	0.667	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCC(=O)O`
ZINC138458029	0.667	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCC(=O)O`
ZINC144395054	0.667	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCCC(=O)O`
ZINC14619628	0.667	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCCCCC(=O)O`
ZINC196749828	0.667	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCC(=O)O`
ZINC2113934076	0.667	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCCC(=O)O`
ZINC2113934082	0.667	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCCCC(=O)O`
ZINC2113934083	0.667	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CCCCC(=O)O`
ZINC2243670	0.667	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCC(=O)O`
ZINC2569203	0.667	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCC(=O)O`
ZINC4798470	0.667	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCCCC(=O)O`
ZINC5973005	0.667	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCC(=O)O`
ZINC71418182	0.667	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCC(=O)CCCCC(=O)O`
ZINC79244776	0.667	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCCCCC(=O)O`
ZINC86037082	0.667	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CCCCCC(=O)O`
ZINC86037089	0.667	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCCCCCC(=O)O`
ZINC86039283	0.667	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCCCC(=O)O`
ZINC11799246	0.636	215.3 Da LogP 2.75 TPSA 40.5	✓ Ro5	✓ Clean	`CCCCN(CCCC)CCCC(=O)O`
ZINC3160730	0.636	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCC(=O)O`
ZINC4582907	0.636	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCC(=O)O`
ZINC4727003	0.636	312.4 Da LogP 4.69 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCC(=O)CCCCCCCC(=O)O`
ZINC86037074	0.636	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)CCCC(=O)O`
ZINC36923853	0.600	201.3 Da LogP 1.50 TPSA 57.6	✓ Ro5	✓ Clean	`CCCCC(=O)N(C)CCCC(=O)O`
ZINC2113934064	0.591	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCC(=O)CCCCCCCCCCCC(=O)O`
ZINC2113934089	0.591	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCC(=O)CCCCCCCCCCC(=O)O`
ZINC2378809	0.591	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCC(=O)CCCCCCC(=O)O`
ZINC1529497	0.588	230.3 Da LogP 3.06 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCC(=O)O`
ZINC1531045	0.588	202.2 Da LogP 2.28 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)O`
ZINC1593115	0.588	216.3 Da LogP 2.67 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCC(=O)O`
ZINC1700020	0.588	244.3 Da LogP 3.45 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCC(=O)O`
ZINC3860440	0.588	258.4 Da LogP 3.84 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCC(=O)O`
ZINC3861298	0.588	286.4 Da LogP 4.62 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCC(=O)O`
ZINC5113062	0.588	272.4 Da LogP 4.23 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCC(=O)O`
ZINC1531062	0.583	226.4 Da LogP 4.55 TPSA 37.3	✓ Ro5	✓ Clean	`CCCC/C=C/CCCCCCCC(=O)O`
ZINC1600675	0.583	232.4 Da LogP 3.94 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCSCCCC(=O)O`
ZINC2387442	0.583	246.4 Da LogP 4.34 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCSCCCCC(=O)O`
ZINC2504617	0.583	240.4 Da LogP 4.94 TPSA 37.3	✓ Ro5	✓ Clean	`CCCC/C=C/CCCCCCCCC(=O)O`
ZINC28539337	0.583	224.3 Da LogP 4.00 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCC#CCCCC(=O)O`
ZINC33822238	0.583	210.3 Da LogP 3.61 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCC#CCCCCCCC(=O)O`
ZINC4529321	0.583	226.4 Da LogP 4.55 TPSA 37.3	✓ Ro5	✓ Clean	`CCCC/C=C\CCCCCCCC(=O)O`
ZINC5260769	0.583	240.4 Da LogP 4.94 TPSA 37.3	✓ Ro5	✓ Clean	`CCCC/C=C\CCCCCCCCC(=O)O`
ZINC88378988	0.583	243.4 Da LogP 3.58 TPSA 49.3	✓ Ro5	✓ Clean	`CCCCCCCCCCNCCCC(=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.