Protein profile

KP13_02109

Homocysteine S-methyltransferase

Genome: KpKP13

Gene: mmuM AHE46109.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GNA7

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Amino acids 310

Annotations 6

Features 20

PDB binders 5

Druggability 0.461

Overview

Basic information about this protein and its source genome.

Accession: KP13_02109
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: mmuM AHE46109.1
Status: annotated
Amino acids: 310
Structure source: AlphaFold + ColabFold

GO:0008270 Binding to a zinc ion (Zn). GO:0009086 OBSOLETE. The chemical reactions and pathways resulting in the de novo formation of L-methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins. GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule. GO:0008898 Catalysis of the reaction: S-adenosyl-L-methionine + L-homocysteine = S-adenosyl-L-homocysteine + L-methionine. GO:0032259 The process in which a methyl group is covalently attached to a molecule. GO:0033528 A cyclic series of interconversions involving S-methyl-L-methionine, S-adenosyl-L-homocysteine, S-adenosyl-L-methionine, L-homocysteine, and L-methionine. Converts the methionine group of adenosylmethionine back to free methionine, and may serve regulate the cellular adenosylmethionine level.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 26.115
Human E-value: 6.88e-13
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 93.75

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 0.461

Structure A0A0H3GNA7

Pocket Pocket 1

P2Rank 0.97

Structure A0A0H3GNA7

Pocket Pocket 1

ColabFold model

FPocket 0.487 · Pocket 1

P2Rank 0.964 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 94 / 4744 genomes with a hit

Normalized 0.02

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

GO:0008270 Binding to a zinc ion (Zn).
GO:0009086 OBSOLETE. The chemical reactions and pathways resulting in the de novo formation of L-methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
GO:0008898 Catalysis of the reaction: S-adenosyl-L-methionine + L-homocysteine = S-adenosyl-L-homocysteine + L-methionine.
GO:0032259 The process in which a methyl group is covalently attached to a molecule.
GO:0033528 A cyclic series of interconversions involving S-methyl-L-methionine, S-adenosyl-L-homocysteine, S-adenosyl-L-methionine, L-homocysteine, and L-methionine. Converts the methionine group of adenosylmethionine back to free methionine, and may serve regulate the cellular adenosylmethionine level.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records

Show feature table

Start	End	DB	Term	Name
20	24	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
1	24	SignalP_EUK	SignalP-noTM	SignalP-noTM
1	309	Gene3D	G3DSA:3.20.20.330	-
1	309	InterPro	IPR036589	Homocysteine-binding domain superfamily
1	7	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
25	310	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
5	310	ProSiteProfiles	PS50970	Homocysteine-binding domain profile.
5	310	InterPro	IPR003726	Homocysteine-binding domain
8	178	PIRSF	PIRSF037505	BHMT
8	178	InterPro	IPR017226	Betaine-homocysteine S-methyltransferase, BHMT
268	309	PIRSF	PIRSF037505	BHMT
268	309	InterPro	IPR017226	Betaine-homocysteine S-methyltransferase, BHMT
17	307	Pfam	PF02574	Homocysteine S-methyltransferase
17	307	InterPro	IPR003726	Homocysteine-binding domain
6	308	SUPERFAMILY	SSF82282	Homocysteine S-methyltransferase
6	308	InterPro	IPR036589	Homocysteine-binding domain superfamily
1	24	Phobius	SIGNAL_PEPTIDE	Signal peptide region
8	19	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
13	308	PANTHER	PTHR46015	ZGC:172121
7	309	FunFam	G3DSA:3.20.20.330:FF:000002	Homocysteine S-methyltransferase

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_A0A0H3GNA7	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02109	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				0.461
9				0.047
3				0.002
5				0.001

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				52.64	0.97
2				2.48	0.055

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				0.487

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				35.48	0.953

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.

67 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
C2F	1Q8J	Q9WYA5	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`C[N@@]1[C@H](CNC2=C1C(=O)NC(=N2)N)CNc3ccc(cc3)C…`
CBH	1LT8	Q93088	235.3 Da LogP 0.78 TPSA 100.6	✓ Ro5	✓ Clean	`C(CCSCC[C@@H](C(=O)O)N)CC(=O)O`
HCS	5DMM	Q47690	135.2 Da LogP -0.28 TPSA 63.3	✓ Ro5	✓ Clean	`C(CS)[C@@H](C(=O)O)N`
SRT	4M3P	Q93088	150.1 Da LogP -2.12 TPSA 115.1	✓ Ro5	✓ Clean	`[C@H]([C@H](C(=O)O)O)(C(=O)O)O`
YT3	3BOF	Q9WYA5	88.9 Da LogP -0.00 TPSA 0.0	✓ Ro5	✓ Clean	`[Y+3]`

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
CHEMBL211229	Q93088	7.92	235.3 Da LogP 0.78 TPSA 100.6	✓ Ro5	✓ Clean	`NC(CCSCCCCC(=O)O)C(=O)O`
CHEMBL488121	Q93088	7.19	263.4 Da LogP 1.41 TPSA 100.6	✓ Ro5	✓ Clean	`CC(C)(CCSCC[C@H](N)C(=O)O)CC(=O)O`
CHEMBL2164724	Q9H2M3	7.11	292.4 Da LogP 0.74 TPSA 126.6	✓ Ro5	✓ Clean	`CC(CCSCC[C@H](N)C(=O)O)CCC(N)C(=O)O`
CHEMBL443372	Q93088	7.08	263.4 Da LogP 1.41 TPSA 100.6	✓ Ro5	✓ Clean	`CC(C)(CCSCCC(N)C(=O)O)CC(=O)O`
CHEMBL211961	Q93088	7.02	253.3 Da LogP 0.34 TPSA 100.6	✓ Ro5	✓ Clean	`NC(CCSCCSCC(=O)O)C(=O)O`
CHEMBL486279	Q93088	6.86	249.3 Da LogP 1.02 TPSA 100.6	✓ Ro5	✓ Clean	`CC(CCSCCC(N)C(=O)O)CC(=O)O`
CHEMBL208607	Q93088	6.70	249.3 Da LogP 1.17 TPSA 100.6	✓ Ro5	✓ Clean	`NC(CCSCCCCCC(=O)O)C(=O)O`
CHEMBL448548	Q93088	6.19	282.2 Da LogP 0.58 TPSA 100.6	✓ Ro5	✓ Clean	`NC(CC[Se]CCCCC(=O)O)C(=O)O`
CHEMBL442625	Q93088	6.15	263.4 Da LogP 1.41 TPSA 100.6	✓ Ro5	✓ Clean	`CC(C)(CCSCC[C@@H](N)C(=O)O)CC(=O)O`
CHEMBL2164725	Q93088	—	306.4 Da LogP 1.13 TPSA 126.6	✓ Ro5	✓ Clean	`CC(C)(CCSCC[C@H](N)C(=O)O)CCC(N)C(=O)O`
CHEMBL2164726	Q9H2M3	—	312.4 Da LogP -0.93 TPSA 149.7	✓ Ro5	✓ Clean	`N[C@@H](CCSCC[S+]([O-])CC[C@H](N)C(=O)O)C(=O)O`
CHEMBL2164727	Q9H2M3	—	328.4 Da LogP -1.91 TPSA 172.8	✓ Ro5	✓ Clean	`N[C@@H](CC[S+]([O-])CC[S+]([O-])CC[C@H](N)C(=O)…`

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
ZINC2005305	1.000	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@@H]1CNc1ccc(C(=O)N[C@…`
ZINC2572666	1.000	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@H]1CNc1ccc(C(=O)N[C@@…`
ZINC4228266	1.000	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@@H]1CNc1ccc(C(=O)N[C@…`
ZINC4228267	1.000	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@H]1CNc1ccc(C(=O)N[C@H…`
ZINC9212425	0.803	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CNc1ccc(C(=O)N[…`
ZINC9212426	0.803	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@H](CNc1ccc(C(=O)N[C…`
ZINC9212427	0.803	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CNc1ccc(C(=O)N[…`
ZINC9212428	0.803	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@H](CNc1ccc(C(=O)N[C…`
ZINC98207756	0.727	330.3 Da LogP 0.39 TPSA 136.4	✓ Ro5	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@@H]1CNc1ccc(C(=O)O)cc1`
ZINC8655682	0.711	487.5 Da LogP -0.34 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CCNc1ccc(C(=O)N…`
ZINC4228235	0.708	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@H](CNc1ccc(C(=O)N[C@@H](…`
ZINC4228236	0.708	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@H](CNc1ccc(C(=O)N[C@H](C…`
ZINC4228237	0.708	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@@H](CNc1ccc(C(=O)N[C@@H]…`
ZINC4228238	0.708	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@@H](CNc1ccc(C(=O)N[C@H](…`
ZINC1674993	0.704	296.4 Da LogP 0.06 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCSCCSCC[C@H](N)C(=O)O)C(=O)O`
ZINC1674994	0.704	296.4 Da LogP 0.06 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCSCCSCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1674996	0.704	296.4 Da LogP 0.06 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCSCCSCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1532902	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC2018106	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
ZINC12359024	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)C(=O)O`
ZINC13533920	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC1532740	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC1549593	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC2013424	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC3581021	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC3860635	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)C(=O)O`
ZINC5783661	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(=O)O`
ZINC6072527	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC8628600	0.671	473.5 Da LogP 0.13 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c([nH]c(N)nc2=O)NC[C@@H]1CCNc1ccc(C(=O)N[C…`
ZINC8628601	0.671	473.5 Da LogP 0.13 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c([nH]c(N)nc2=O)NC[C@H]1CCNc1ccc(C(=O)N[C@…`
ZINC3593496	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC3593497	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC4228243	0.645	457.4 Da LogP -0.52 TPSA 194.0	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N1CN(c3ccc(C(=O)N[C@@H](CCC(…`
ZINC4228244	0.645	457.4 Da LogP -0.52 TPSA 194.0	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N1CN(c3ccc(C(=O)N[C@H](CCC(=…`
ZINC4654260	0.645	457.4 Da LogP -0.52 TPSA 194.0	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N1CN(c3ccc(C(=O)N[C@@H](CCC(…`
ZINC8618631	0.645	459.5 Da LogP 0.11 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@H](CCNc1ccc(C(=O)N[C@@H]…`
ZINC8627114	0.645	459.5 Da LogP 0.11 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@@H](CCNc1ccc(C(=O)N[C@@H…`
ZINC4654270	0.632	471.4 Da LogP -0.36 TPSA 211.0	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N1C(=O)N(c3ccc(C(=O)N[C@@H](…`
ZINC4654271	0.632	471.4 Da LogP -0.36 TPSA 211.0	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N1C(=O)N(c3ccc(C(=O)N[C@@H](…`
ZINC1661158	0.630	234.3 Da LogP 2.23 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCSCCCCC(=O)O`
ZINC14686440	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…`
ZINC14686442	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=O…`
ZINC14686444	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=…`
ZINC1529407	0.621	222.3 Da LogP -1.07 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCSC[C@@H](N)C(=O)O)C(=O)O`
ZINC1532680	0.621	222.3 Da LogP -1.07 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCSC[C@H](N)C(=O)O)C(=O)O`
ZINC1708207	0.621	222.3 Da LogP -1.07 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCSC[C@H](N)C(=O)O)C(=O)O`
ZINC1708208	0.621	222.3 Da LogP -1.07 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CSCC[C@@H](N)C(=O)O)C(=O)O`
ZINC3055005	0.619	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@H](N)C(=O)O)C(=O)O`
ZINC3055007	0.619	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC3055010	0.619	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCC[C@@H](N)C(=O)O)C(=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.