Protein profile

KP13_03382

Methylthioribose-1-phosphate isomerase

Genome: KpKP13

Gene: AHE45761.1 mtnA Structure source: AlphaFold + ColabFold UniProt A0A0H3GPS7

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Amino acids 342

Annotations 5

Features 16

PDB binders 5

Druggability 0.86

Overview

Basic information about this protein and its source genome.

Accession: KP13_03382
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE45761.1 mtnA
Status: annotated
Amino acids: 342
Structure source: AlphaFold + ColabFold

5.3.1.23

GO:0044249 OBSOLETE. The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GO:0044237 OBSOLETE. The chemical reactions and pathways by which individual cells transform chemical substances. GO:0046523 Catalysis of the reaction: S-methyl-5-thio-alpha-D-ribose 1-phosphate = S-methyl-5-thio-D-ribulose 1-phosphate. 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 (%): 41.16
Human E-value: 8.36e-71
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 48.308
DEG E-value: 4.32e-83
Localization: Cytoplasmic
ColabFold pLDDT: 96.02

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 0.86

Structure A0A0H3GPS7

Pocket Pocket 1

P2Rank 0.851

Structure A0A0H3GPS7

Pocket Pocket 1

ColabFold model

FPocket 0.495 · Pocket 7

P2Rank 0.851 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 76 / 4744 genomes with a hit

Normalized 0.016

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

5.3.1.23

Gene Ontology (GO)

GO:0044249 OBSOLETE. The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
GO:0044237 OBSOLETE. The chemical reactions and pathways by which individual cells transform chemical substances.
GO:0046523 Catalysis of the reaction: S-methyl-5-thio-alpha-D-ribose 1-phosphate = S-methyl-5-thio-D-ribulose 1-phosphate.
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.

16 records

Show feature table

Start	End	DB	Term	Name
6	337	PANTHER	PTHR43475	METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE
8	328	NCBIfam	TIGR00512	S-methyl-5-thioribose-1-phosphate isomerase
8	328	InterPro	IPR005251	Methylthioribose-1-phosphate isomerase
6	336	Hamap	MF_01678	Putative methylthioribose-1-phosphate isomerase [mtnA].
6	336	InterPro	IPR005251	Methylthioribose-1-phosphate isomerase
1	174	Gene3D	G3DSA:1.20.120.420	-
1	174	InterPro	IPR027363	Methylthioribose-1-phosphate isomerase, N-terminal
175	335	Gene3D	G3DSA:3.40.50.10470	-
175	335	InterPro	IPR042529	Initiation factor 2B-like, C-terminal
140	336	FunFam	G3DSA:3.40.50.10470:FF:000006	Methylthioribose-1-phosphate isomerase
8	332	SUPERFAMILY	SSF100950	NagB/RpiA/CoA transferase-like
8	332	InterPro	IPR037171	NagB/RpiA transferase-like
39	329	NCBIfam	TIGR00524	S-methyl-5-thioribose-1-phosphate isomerase
39	329	InterPro	IPR011559	Initiation factor 2B alpha/beta/delta
48	329	Pfam	PF01008	Initiation factor 2 subunit family
48	329	InterPro	IPR000649	Initiation factor 2B-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_A0A0H3GPS7	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_03382	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
1				0.86
11				0.431
8				0.401

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				15.01	0.742
2				1.14	0.009

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
7				0.495
12				0.316
1				0.219

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				14.9	0.738

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.

55 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
C7B	6CAJ	P49770	451.4 Da LogP 3.99 TPSA 76.7	✓ Ro5	✓ Clean	`c1cc(ccc1OCC(=O)NC2CCC(CC2)NC(=O)COc3ccc(cc3)Cl…`
M6P	7KMA	Q14232	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`C([C@@H]1[C@H]([C@@H]([C@@H]([C@H](O1)O)O)O)O)O…`
MRU	2YVK	O31662	260.2 Da LogP -1.25 TPSA 124.3	✓ Ro5	✓ Clean	`CSC[C@H]([C@H](C(=O)COP(=O)(O)O)O)O`
RI2	5YFS	O57947	310.1 Da LogP -2.35 TPSA 183.2	1 viol.	✓ Clean	`C([C@@H]1[C@H]([C@H]([C@H](O1)OP(=O)(O)O)O)O)OP…`
RUB	5YFJ	O57947	310.1 Da LogP -2.50 TPSA 191.0	1 viol.	✓ Clean	`C([C@H]([C@H](C(=O)COP(=O)(O)O)O)O)OP(=O)(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
ZINC100081898	1.000	451.4 Da LogP 3.99 TPSA 76.7	✓ Ro5	✓ Clean	`O=C(COc1ccc(Cl)cc1)N[C@H]1CC[C@H](NC(=O)COc2ccc…`
ZINC100351935	1.000	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@H](O)[C@H](O)[C@H](O)[C@@…`
ZINC1529564	1.000	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@@H](O)[C@H](O)[C@H](O)[C@…`
ZINC1532533	1.000	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@H](O)[C@@H](O)[C@H](O)[C@…`
ZINC1532857	1.000	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@@H](O)[C@@H](O)[C@H](O)[C…`
ZINC245239931	1.000	451.4 Da LogP 3.99 TPSA 76.7	✓ Ro5	✓ Clean	`O=C(COc1ccc(Cl)cc1)N[C@H]1CC[C@H](NC(=O)COc2ccc…`
ZINC3581460	1.000	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@@H](O)[C@@H](O)[C@H](O)[C…`
ZINC38276879	1.000	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](O)[C@@H](O)[C@H](O)[C@…`
ZINC38276880	1.000	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O)[C@@H](O)[C@H](O)[C@H…`
ZINC3869397	1.000	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[C…`
ZINC3870277	1.000	310.1 Da LogP -2.50 TPSA 191.0	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC3875374	1.000	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](O)[C@H](O)[C@@H](O)[C@…`
ZINC3875375	1.000	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@…`
ZINC4095545	1.000	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](O)[C@H](O)[C@@H](O)[C@…`
ZINC4095546	1.000	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@H…`
ZINC4096188	1.000	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O)[C@@H](O)[C@@H](O)[C@…`
ZINC4702158	1.000	225.7 Da LogP 2.00 TPSA 38.3	✓ Ro5	✓ Clean	`O=C(COc1ccc(Cl)cc1)NC1CC1`
ZINC671772	1.000	451.4 Da LogP 3.99 TPSA 76.7	✓ Ro5	✓ Clean	`O=C(COc1ccc(Cl)cc1)NC1CCC(NC(=O)COc2ccc(Cl)cc2)…`
ZINC8551507	1.000	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@H](O)[C@@H](O)[C@H](O)[C@…`
ZINC12504154	0.962	230.1 Da LogP -2.47 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O)[C@@H](O)[C@@H]1O`
ZINC1532546	0.962	230.1 Da LogP -2.47 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@H](O)[C@@H](O)[C@H]1O`
ZINC4096190	0.962	230.1 Da LogP -2.47 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O)[C@H](O)[C@@H]1O`
ZINC4228241	0.962	230.1 Da LogP -2.47 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](O)[C@H](O)[C@@H]1O`
ZINC4521831	0.962	230.1 Da LogP -2.47 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](O)[C@@H](O)[C@@H]1O`
ZINC146558	0.909	253.7 Da LogP 2.78 TPSA 38.3	✓ Ro5	✓ Clean	`O=C(COc1ccc(Cl)cc1)NC1CCCC1`
ZINC3387598	0.886	329.8 Da LogP 3.23 TPSA 55.4	✓ Ro5	✓ Clean	`O=C(COc1ccc(C(=O)c2ccc(Cl)cc2)cc1)NC1CC1`
ZINC1016959	0.882	281.8 Da LogP 3.56 TPSA 38.3	✓ Ro5	✓ Clean	`O=C(COc1ccc(Cl)cc1)NC1CCCCCC1`
ZINC443437	0.882	295.8 Da LogP 3.95 TPSA 38.3	✓ Ro5	✓ Clean	`O=C(COc1ccc(Cl)cc1)NC1CCCCCCC1`
ZINC68802	0.882	267.8 Da LogP 3.17 TPSA 38.3	✓ Ro5	✓ Clean	`O=C(COc1ccc(Cl)cc1)NC1CCCCC1`
ZINC51172603	0.861	281.8 Da LogP 3.41 TPSA 38.3	✓ Ro5	✓ Clean	`CC1CCC(NC(=O)COc2ccc(Cl)cc2)CC1`
ZINC7035958	0.838	357.8 Da LogP 4.01 TPSA 55.4	✓ Ro5	✓ Clean	`O=C(COc1ccc(C(=O)c2ccc(Cl)cc2)cc1)NC1CCCC1`
ZINC3402618	0.811	283.7 Da LogP 1.54 TPSA 64.6	✓ Ro5	✓ Clean	`O=C(COC(=O)COc1ccc(Cl)cc1)NC1CC1`
ZINC36880012	0.811	281.7 Da LogP 2.35 TPSA 55.4	✓ Ro5	✓ Clean	`O=C1CCC(NC(=O)COc2ccc(Cl)cc2)CC1`
ZINC12502210	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)[C@@H](O)COP(=O…`
ZINC12502212	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)[C@H](O)COP(=O)…`
ZINC12502214	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@@H](O)[C@@H](O)COP(=…`
ZINC12502216	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@@H](O)[C@H](O)COP(=O…`
ZINC4523251	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@@H](O)[C@@H](O)COP(…`
ZINC4523255	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@@H](O)[C@H](O)COP(=…`
ZINC4523257	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)[C@@H](O)COP(=…`
ZINC4523259	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)[C@H](O)COP(=O…`
ZINC253405977	0.789	317.8 Da LogP 1.41 TPSA 72.5	✓ Ro5	✓ Clean	`O=C(COc1ccc(Cl)cc1)NC1CCS(=O)(=O)CC1`
ZINC12376161	0.775	343.9 Da LogP 4.56 TPSA 38.3	✓ Ro5	✓ Clean	`O=C(COc1ccc(Cl)cc1)NC1CCC(c2ccccc2)CC1`
ZINC16605351	0.769	282.8 Da LogP 1.93 TPSA 41.6	✓ Ro5	✓ Clean	`CN1CCC(NC(=O)COc2ccc(Cl)cc2)CC1`
ZINC14162823	0.750	308.8 Da LogP 2.46 TPSA 41.6	✓ Ro5	✓ Clean	`O=C(COc1ccc(Cl)cc1)NC1CCN(C2CC2)CC1`
ZINC14187435	0.750	310.8 Da LogP 1.85 TPSA 58.6	✓ Ro5	✓ Clean	`CC(=O)N1CCC(NC(=O)COc2ccc(Cl)cc2)CC1`
ZINC3219531	0.744	311.8 Da LogP 2.32 TPSA 64.6	✓ Ro5	✓ Clean	`O=C(COC(=O)COc1ccc(Cl)cc1)NC1CCCC1`
ZINC13516910	0.733	244.1 Da LogP -2.42 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@@H](CO)[C@@H](O)[C@H]1O`
ZINC2562340	0.733	244.1 Da LogP -2.42 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@@H](CO)[C@H](O)[C@H]1O`
ZINC13715791	0.732	358.8 Da LogP 3.18 TPSA 67.4	✓ Ro5	✓ Clean	`O=C(COc1ccc(Cl)cc1)Nc1ccc(CC(=O)NC2CC2)cc1`

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.