Protein profile

VK055_0305

cobalamin-independent synthase, Catalytic domainprotein

Genome: KpATCC43816

Gene: AIK78931.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GU58

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Amino acids 343

Annotations 4

Features 11

PDB binders 6

Druggability 0.866

Overview

Basic information about this protein and its source genome.

Accession: VK055_0305
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK78931.1
Status: annotated
Amino acids: 343
Structure source: AlphaFold + ColabFold

GO:0008270 Binding to a zinc ion (Zn). GO:0003871 Catalysis of the reaction: 5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = L-methionine + tetrahydropteroyltri-L-glutamate. 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: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): Y
DEG identity (%): 86.813
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 97.31

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 0.866

Structure A0A0H3GU58

Pocket Pocket 1

P2Rank 0.845

Structure A0A0H3GU58

Pocket Pocket 1

ColabFold model

FPocket 0.925 · Pocket 1

P2Rank 0.842 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 93 / 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.

4 GO

Gene Ontology (GO)

GO:0008270 Binding to a zinc ion (Zn).
GO:0003871 Catalysis of the reaction: 5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = L-methionine + tetrahydropteroyltri-L-glutamate.
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:0032259 The process in which a methyl group is covalently attached to a molecule.

Sequence Features

Domain/signature hits from InterPro and related databases.

11 records

Show feature table

Start	End	DB	Term	Name
1	343	Gene3D	G3DSA:3.20.20.210	-
1	343	InterPro	IPR038071	UROD/MetE-like superfamily
5	330	Pfam	PF01717	Cobalamin-independent synthase, Catalytic domain
5	330	InterPro	IPR002629	Cobalamin-independent methionine synthase MetE, C-terminal/archaeal
7	341	SUPERFAMILY	SSF51726	UROD/MetE-like
7	341	InterPro	IPR038071	UROD/MetE-like superfamily
6	335	CDD	cd03311	CIMS_C_terminal_like
6	335	InterPro	IPR002629	Cobalamin-independent methionine synthase MetE, C-terminal/archaeal
1	343	PIRSF	PIRSF005632	Met_synth_catalytic
1	343	InterPro	IPR016456	Predicted cobalamin-independent methionine synthase, catalytic subunit
5	341	PANTHER	PTHR30519	5-METHYLTETRAHYDROPTEROYLTRIGLUTAMATE--HOMOCYSTEINE 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_A0A0H3GU58	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_0305	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				0.866

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	15.0	0.741
2	3.89	0.153
3	1.16	0.009
4	0.77	0.002

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				0.925

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	15.41	0.753
2	5.05	0.23
3	0.92	0.004

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.

56 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
39S	4QQU	P82610	703.7 Da LogP -1.58 TPSA 344.4	3 viol.	✓ Clean	`c1cc(ccc1C(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)N[C…`
C2F	1U1J	O50008	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…`
HCS	1U22	O50008	135.2 Da LogP -0.28 TPSA 63.3	✓ Ro5	✓ Clean	`C(CS)[C@@H](C(=O)O)N`
MRY	1T7L	Q9X112	122.1 Da LogP -2.31 TPSA 80.9	✓ Ro5	✓ Clean	`C([C@H]([C@H](CO)O)O)O`
MTX	4L6H	P82610	454.4 Da LogP 0.27 TPSA 210.5	✓ Ro5	✓ Clean	`CN(Cc1cnc2c(n1)c(nc(n2)N)N)c3ccc(cc3)C(=O)N[C@@…`
THG	1U22	O50008	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC[C@H]2C…`

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
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…`
ZINC13604299	0.825	439.5 Da LogP 0.14 TPSA 199.3	✓ Ro5	✓ Clean	`CN(Cc1cnc2nc(N)nc(N)c2n1)c1ccc(C(=O)N[C@@H](CCC…`
ZINC13284373	0.813	453.5 Da LogP 0.53 TPSA 199.3	✓ Ro5	✓ Clean	`CN(Cc1cnc2nc(N)nc(N)c2n1)c1ccc(C(=O)N[C@@H](CCC…`
ZINC8627939	0.813	453.5 Da LogP 0.53 TPSA 199.3	✓ Ro5	✓ Clean	`CN(Cc1cnc2nc(N)nc(N)c2n1)c1ccc(C(=O)N[C@H](CCCC…`
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…`
ZINC255970296	0.794	478.5 Da LogP 0.05 TPSA 226.7	✓ Ro5	Alert	`CN(Cc1cnc2nc(N)nc(N)c2n1)c1ccc(C(=O)N[C@@H](CCC…`
ZINC22062147	0.785	482.5 Da LogP 0.45 TPSA 188.5	1 viol.	✓ Clean	`COC(=O)CC[C@H](NC(=O)c1ccc(N(C)Cc2cnc3nc(N)nc(N…`
ZINC1734471	0.765	488.9 Da LogP 0.92 TPSA 210.5	✓ Ro5	✓ Clean	`CN(Cc1cnc2nc(N)nc(N)c2n1)c1ccc(C(=O)N[C@@H](CCC…`
ZINC8628726	0.765	488.9 Da LogP 0.92 TPSA 210.5	✓ Ro5	✓ Clean	`CN(Cc1cnc2nc(N)nc(N)c2n1)c1ccc(C(=O)N[C@H](CCC(…`
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`
ZINC1560410190	0.712	453.4 Da LogP 0.43 TPSA 210.5	✓ Ro5	✓ Clean	`CN(Cc1cnc2nc(N)nc(N)c2n1)c1ccc(C(=O)N[C](CCC(=O…`
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](…`
ZINC404265	0.683	325.3 Da LogP 0.92 TPSA 144.1	✓ Ro5	✓ Clean	`CN(Cc1cnc2nc(N)nc(N)c2n1)c1ccc(C(=O)O)cc1`
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@…`
ZINC1720422	0.651	339.4 Da LogP 1.01 TPSA 133.1	✓ Ro5	✓ Clean	`COC(=O)c1ccc(N(C)Cc2cnc3nc(N)nc(N)c3n2)cc1`
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](…`
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`
ZINC100055463	0.615	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC100064885	0.615	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC1653968	0.615	353.4 Da LogP 1.40 TPSA 133.1	✓ Ro5	✓ Clean	`CCOC(=O)c1ccc(N(C)Cc2cnc3nc(N)nc(N)c3n2)cc1`
ZINC17780060	0.615	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@@H](O)[C@H](O)C(O)[C@H](O)[C@H](O)CO`
ZINC17952732	0.615	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)C(O)[C@H](O)[C@H](O)CO`
ZINC18042331	0.615	242.2 Da LogP -4.86 TPSA 161.8	1 viol.	✓ Clean	`OC[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H]…`
ZINC18120313	0.615	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@H](O)C(O)[C@H](O)[C@H](O)CO`
ZINC3979006	0.615	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@@H](O)[C@@H](O)C(O)[C@H](O)[C@H](O)CO`
ZINC4403103	0.615	242.2 Da LogP -4.86 TPSA 161.8	1 viol.	✓ Clean	`OC[C@@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H…`
ZINC4403105	0.615	242.2 Da LogP -4.86 TPSA 161.8	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H…`
ZINC4403107	0.615	242.2 Da LogP -4.86 TPSA 161.8	1 viol.	✓ Clean	`OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)[C@…`
ZINC9212412	0.615	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)C(O)[C@H](O)[C@@H](O)CO`
ZINC4228265	0.605	443.4 Da LogP 0.01 TPSA 211.9	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N=C(CNc1ccc(C(=O)N[C@@H](CCC…`
ZINC4658144	0.605	443.5 Da LogP 0.62 TPSA 187.5	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)C[C@@H](CCc1ccc(C(=O)N[C@H](…`

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.