Target Pathogen

Overview

Basic information about this protein and its source genome.

Accession: HT085_RS00185
Assembly: Neisseria gonorrhoeae strain TUM19854 chromosome, complete genome
Gene: WHOF_00390 WHOF_00035C N776_09150 ESCNG_30015 TUM19854C_00320 NGK_0047 miaB E8M63_03345
Status: annotated
Amino acids: 442
Structure source: AlphaFold

EC

2.8.4.3

GO

GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0046872 Binding to a metal ion. GO:0035597 Catalysis of the reaction: N(6)-dimethylallyladenosine(37) in tRNA + [sulfur carrier]-SH + AH2 + 2 S-adenosyl-L-methionine = 2-methylsulfanyl-N(6)-dimethylallyladenosine(37) in tRNA + [sulfur carrier]-H + 5'-deoxyadenosine + L-methionine + A + S-adenosyl-L-homocysteine + 2 H+.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Gut microbiome off-target: hit
Essential (DEG): N
Localization: Cytoplasmic

Selected Druggability evidence

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 High

Structure –

Pocket –

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)

1

2.8.4.3

Gene Ontology (GO)

4

GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0046872 Binding to a metal ion.
GO:0035597 Catalysis of the reaction: N(6)-dimethylallyladenosine(37) in tRNA + [sulfur carrier]-SH + AH2 + 2 S-adenosyl-L-methionine = 2-methylsulfanyl-N(6)-dimethylallyladenosine(37) in tRNA + [sulfur carrier]-H + 5'-deoxyadenosine + L-methionine + A + S-adenosyl-L-homocysteine + 2 H+.

Sequence Features

Domain/signature hits from InterPro and related databases.

36 records

Show feature table

Start	End	DB	Term	Name
3	440	NCBIfam	TIGR01574	tRNA (N6-isopentenyl adenosine(37)-C2)-methylthiotransferase MiaB
2	130	FunFam	G3DSA:3.40.50.12160:FF:000001	tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase
1	441	SFLD	SFLDF00273	(dimethylallyl)adenosine tRNA methylthiotransferase (MiaB-like)
1	441	InterPro	IPR006463	tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase MiaB
378	440	Pfam	PF01938	TRAM domain
378	440	InterPro	IPR002792	TRAM domain
378	441	ProSiteProfiles	PS50926	TRAM domain profile.
378	441	InterPro	IPR002792	TRAM domain
2	131	Gene3D	G3DSA:3.40.50.12160	-
2	131	InterPro	IPR038135	Methylthiotransferase, N-terminal domain superfamily
145	381	FunFam	G3DSA:3.80.30.20:FF:000001	tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase 2
37	354	SFLD	SFLDG01082	B12-binding domain containing
143	375	ProSiteProfiles	PS51918	Radical SAM core domain profile.
143	375	InterPro	IPR007197	Radical SAM
1	441	SFLD	SFLDG01061	methylthiotransferase
1	441	InterPro	IPR005839	Methylthiotransferase
151	171	ProSitePatterns	PS01278	Methylthiotransferase radical SAM domain signature.
151	171	InterPro	IPR020612	Methylthiotransferase, conserved site
355	375	Coils	Coil	Coil
145	380	Gene3D	G3DSA:3.80.30.20	tm_1862 like domain
145	380	InterPro	IPR023404	Radical SAM, alpha/beta horseshoe
156	364	CDD	cd01335	Radical_SAM
129	371	SUPERFAMILY	SSF102114	Radical SAM enzymes
2	120	ProSiteProfiles	PS51449	Methylthiotransferase N-terminal domain profile.
2	120	InterPro	IPR013848	Methylthiotransferase, N-terminal
2	441	Hamap	MF_01864	tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase [miaB].
2	441	InterPro	IPR006463	tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase MiaB
151	325	Pfam	PF04055	Radical SAM superfamily
151	325	InterPro	IPR007197	Radical SAM
3	437	NCBIfam	TIGR00089	MiaB/RimO family radical SAM methylthiotransferase
3	437	InterPro	IPR005839	Methylthiotransferase
147	364	SMART	SM00729	MiaB
147	364	InterPro	IPR006638	Elp3/MiaA/NifB-like, radical SAM core domain
3	104	Pfam	PF00919	Uncharacterized protein family UPF0004
3	104	InterPro	IPR013848	Methylthiotransferase, N-terminal
2	441	PANTHER	PTHR43020	CDK5 REGULATORY SUBUNIT-ASSOCIATED PROTEIN 1

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 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold HT085_RS00185	AlphaFold	—	—	full sequence	—	Viewing

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				0.718

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				52.7	0.97
2				4.38	0.151

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.

15 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
CXS	2QGQ	Q9X2H6	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`C1CCC(CC1)NCCCS(=O)(=O)O`
FS5	4JC0	Q9X2H6	863.6 Da LogP 8.41 TPSA 0.0	2 viol.	✓ Clean	`S(SS[Fe]12[S]3[Fe]4[S]1[Fe]5[S]4[Fe]3[S]25)SS[F…`

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
ZINC2004372	1.000	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCNC1CCCCC1`
ZINC38364153	0.926	235.3 Da LogP 1.58 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCNC1CCCCC1`
ZINC1710230	0.786	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCNC1CCCCC1`
ZINC5188799	0.630	280.5 Da LogP 4.39 TPSA 24.1	✓ Ro5	✓ Clean	`C(CCCNC1CCCCC1)CCNC1CCCCC1`
ZINC2509149	0.531	211.4 Da LogP 4.27 TPSA 12.0	✓ Ro5	✓ Clean	`CCCCCCCCNC1CCCCC1`
ZINC130127586	0.529	260.4 Da LogP 1.38 TPSA 58.2	✓ Ro5	✓ Clean	`O=S(=O)(NCCNC1CCCCCC1)C1CC1`
ZINC19367005	0.519	224.4 Da LogP 2.83 TPSA 24.1	✓ Ro5	✓ Clean	`C1CCC(NCCNC2CCCCC2)CC1`
ZINC1672446	0.500	228.3 Da LogP 1.49 TPSA 75.3	✓ Ro5	✓ Clean	`N[C@@H](CCCCNC1CCCCC1)C(=O)O`
ZINC2168583	0.500	237.3 Da LogP 0.16 TPSA 86.6	✓ Ro5	✓ Clean	`O=S(=O)(O)C[C@@H](O)CNC1CCCCC1`
ZINC2168584	0.500	237.3 Da LogP 0.16 TPSA 86.6	✓ Ro5	✓ Clean	`O=S(=O)(O)C[C@H](O)CNC1CCCCC1`
ZINC236994621	0.500	290.4 Da LogP 0.85 TPSA 75.3	✓ Ro5	✓ Clean	`CCS(=O)(=O)CC(=O)NCCNC1CCCCCC1`
ZINC44655186	0.500	213.4 Da LogP 3.12 TPSA 21.3	✓ Ro5	✓ Clean	`COCCCCNC1CCCCCCC1`
ZINC5840523	0.500	228.3 Da LogP 1.49 TPSA 75.3	✓ Ro5	✓ Clean	`N[C@H](CCCCNC1CCCCC1)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.

HT085_RS00185