KpKP13 Protein target profile

Signal peptidase I

Accession: KP13_00812

Gene: lepB AHE43176.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GTU0

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Length 321

Pocket druggability (P2Rank · AlphaFold DB model) 0.15

Direct ligand evidence 0 29 total records

Functional annotation 1 EC 7 GO

Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.73. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target: No hit
Gut microbiome similarity: 2.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 90.343 Higher values support similarity to known essential genes.
DEG E-value: 0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 90.67 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.15

Structure A0A0H3GTU0

Pocket Pocket 1

Druggability (FPocket) 0.733

Structure A0A0H3GTU0

Pocket Pocket 1

ColabFold model

P2Rank 0.383 · Pocket 1

FPocket 0.94 · Pocket 9

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 125 / 4744 genomes with a hit

Prevalence 2.6%

Sequence

Primary amino-acid sequence viewer.

MFALILVIATLVTGVLWCLDKFIFAPKRRERQAAAQAATGEQLDKKTLKKVGPKPGWLETGASVFPVLAIVLVVRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPEDPRLDYIKRAVGLPGDKVTYDPVAKQVTIQPGCSSGQACGNALPVTYSNVEPSDFVQTFSRSNGGEASSGFWQLPKGETKADGIRLTERQETLGDVTHRILMVPIAQDQVGMYYHQSGLPLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGKATAIWMSFEKQEGEWPTGVRLSRIGGIH

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Subcellular localization

Localization: CytoplasmicMembrane

Enzyme Commission (EC)

3.4.21.89

Gene Ontology (GO)

GO:0004252 Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
GO:0006465 OBSOLETE. The proteolytic removal of a signal peptide from a protein during or after transport to a specific location in the cell.
GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
GO:0008236 Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0009003 An endopeptidase that cleaves a hydrophobic, N-terminal signal or leader sequences from mitochondrial, secreted and periplasmic proteins.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

34 records

Show feature table

Start	End	DB	Term	Name
57	79	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
80	294	CDD	cd06530	S26_SPase_I
80	294	InterPro	IPR019533	Peptidase S26
1	18	Phobius	SIGNAL_PEPTIDE	Signal peptide region
259	301	NCBIfam	TIGR02227	signal peptidase I
259	301	InterPro	IPR000223	Peptidase S26A, signal peptidase I
63	156	NCBIfam	TIGR02227	signal peptidase I
63	156	InterPro	IPR000223	Peptidase S26A, signal peptidase I
2	13	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
73	317	Gene3D	G3DSA:2.10.109.10	Umud Fragment, subunit A
141	153	PRINTS	PR00727	Bacterial leader peptidase 1 (S26A) family signature
141	153	InterPro	IPR000223	Peptidase S26A, signal peptidase I
261	280	PRINTS	PR00727	Bacterial leader peptidase 1 (S26A) family signature
261	280	InterPro	IPR000223	Peptidase S26A, signal peptidase I
77	93	PRINTS	PR00727	Bacterial leader peptidase 1 (S26A) family signature
77	93	InterPro	IPR000223	Peptidase S26A, signal peptidase I
57	299	Pfam	PF10502	Signal peptidase, peptidase S26
57	299	InterPro	IPR019533	Peptidase S26
14	18	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
59	303	PANTHER	PTHR43390	SIGNAL PEPTIDASE I
59	303	InterPro	IPR000223	Peptidase S26A, signal peptidase I
152	260	Gene3D	G3DSA:2.170.230.10	-
152	260	InterPro	IPR019766	Signal peptidase I, all-beta subdomain
266	279	ProSitePatterns	PS00761	Signal peptidases I signature 3.
266	279	InterPro	IPR019758	Peptidase S26A, signal peptidase I, conserved site
1	1	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
75	320	SUPERFAMILY	SSF51306	LexA/Signal peptidase
75	320	InterPro	IPR036286	LexA/Signal peptidase-like superfamily
143	155	ProSitePatterns	PS00760	Signal peptidases I lysine active site.
143	155	InterPro	IPR019757	Peptidase S26A, signal peptidase I, lysine active site
19	321	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
4	26	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
86	93	ProSitePatterns	PS00501	Signal peptidases I serine active site.
86	93	InterPro	IPR019756	Peptidase S26A, signal peptidase I, serine active site

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low

How colors and pocket overlays are used

Uniform protein color marks the displayed model as a single molecular object.

Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.

Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.

'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.

'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.

'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.

Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1

0.15

Likely same site as FPocket 1 2.9 Å 11 shared residues 100% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.091

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Surrounding area

Pocket 3 P2Rank #3

0.005

Likely same site as FPocket 4 4.9 Å 4 shared residues 100% of smaller site

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Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #1

0.733 Unusual size

Likely same site as P2Rank 1 2.9 Å 11 shared residues 100% of smaller site

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Surrounding area

Pocket 2 FPocket #4

0.413

Likely same site as P2Rank 3 4.9 Å 4 shared residues 100% of smaller site

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Surrounding area

Residue sets

UniProt: Active site:146-146

UniProt: Active site:91-91

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1

0.383

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Surrounding area

Pocket 2 P2Rank #2

0.066

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Surrounding area

Pocket 3 P2Rank #3

0.015

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Surrounding area

All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold DB AF_A0A0H3GTU0	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_00812	ColabFold	—	—	full sequence	—	Loaded

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.

29 records

Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records

Transferred evidence 29 records from similar proteins

Structural ligands 1 0 loaded crystals

Measured bioactivity 28 direct and transferred ChEMBL records

Proposed compounds 0 similarity-based ZINC candidates

Best available ligand signal

CZD PDB via homolog 892.1 Da · LogP 2.05 · TPSA 282.9 Open detail RCSB PDB

CHEMBL5410707 ChEMBL via homolog · pchembl 9.36 (~0.4 nM) Detail ChEMBL

CHEMBL3947604 ChEMBL via homolog · pchembl 8.22 (~6.0 nM) Detail ChEMBL

CHEMBL4284736 ChEMBL via homolog · pchembl 8.22 (~6.0 nM) Detail ChEMBL

CHEMBL3922978 ChEMBL via homolog · pchembl 7.92 (~12.0 nM) Detail ChEMBL

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, 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
CZD RCSB PDB	6B88	P00803	892.1 Da LogP 2.05 TPSA 282.9	3 viol.	✓ Clean	`[H]/N=C\CNC(=O)[C@@H]1Cc2ccc(c(c2)-c3cc(ccc3OCC…`

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
CHEMBL5410707 ChEMBL	P00803	9.36 ~0.4 nM	890.1 Da LogP 1.92 TPSA 282.8	3 viol.	✓ Clean	`Cc1nc(-c2ccc(C(C)(C)C)cc2)ncc1C(=O)N[C@@H](CCN)…`
CHEMBL3947604 ChEMBL	P00803	8.22 ~6.0 nM	765.7 Da LogP -0.49 TPSA 266.5	2 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N3CC(CN)C[C@H]3C(=O)N[C…`
CHEMBL4284736 ChEMBL	P00803	8.22 ~6.0 nM	765.7 Da LogP -0.49 TPSA 266.5	2 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N3CC(CN)C[C@H]3C(=O)N[C…`
CHEMBL3922978 ChEMBL	P00803	7.92 ~12.0 nM	870.9 Da LogP 3.58 TPSA 218.5	2 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N3CCC[C@H]3C(=O)N[C@H](…`
CHEMBL4283840 ChEMBL	P00803	7.77 ~17.0 nM	887.9 Da LogP 2.82 TPSA 253.3	2 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N[C@@H](CCCN)C(=O)N[C@H…`
CHEMBL3934222 ChEMBL	P00803	7.75 ~17.8 nM	899.9 Da LogP 2.77 TPSA 244.5	2 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N3CC(CN)C[C@H]3C(=O)N[C…`
CHEMBL4283678 ChEMBL	P00803	7.54 ~28.8 nM	925.9 Da LogP 1.39 TPSA 278.8	3 viol.	✓ Clean	`CCCCCCc1ccc(-c2nc3cc(C(=O)N[C@@H](CCCN)C(=O)N[C…`
CHEMBL1784531 ChEMBL	P00803	7.41 ~38.9 nM	881.1 Da LogP 3.82 TPSA 255.0	2 viol.	✓ Clean	`CCCCCCCCCCCCCCCC(=O)N(C)[C@H](CO)C(=O)N[C@H](C)…`
CHEMBL4282733 ChEMBL	P00803	7.39 ~40.7 nM	926.9 Da LogP 0.56 TPSA 280.0	3 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N[C@@H](CCCNC(=N)N)C(=O…`
CHEMBL4291540 ChEMBL	P00803	7.39 ~40.7 nM	834.8 Da LogP -0.56 TPSA 263.0	3 viol.	✓ Clean	`CCCCCCC#Cc1cncc(C(=O)N[C@@H](CCCN)C(=O)N[C@H](C…`
CHEMBL4291025 ChEMBL	P00803	7.38 ~41.7 nM	856.8 Da LogP 0.26 TPSA 244.2	3 viol.	✓ Clean	`CCCCc1ccc(-c2ccc(C(=O)N[C@@H](CCCN)C(=O)N[C@H](…`
CHEMBL3957297 ChEMBL	P00803	7.32 ~47.9 nM	760.8 Da LogP 1.62 TPSA 218.5	2 viol.	✓ Clean	`CCCCCCCCCC(=O)N1CCC[C@H]1C(=O)N[C@H](C(=O)N[C@@…`
CHEMBL4294422 ChEMBL	P00803	7.28 ~52.5 nM	753.7 Da LogP -0.44 TPSA 275.3	2 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N[C@@H](CCCN)C(=O)N[C@H…`
CHEMBL4292925 ChEMBL	P00803	7.14 ~72.4 nM	801.7 Da LogP -0.61 TPSA 250.1	3 viol.	✓ Clean	`C[C@@H]1NC(=O)[C@@H](NC(=O)[C@H](C)NC(=O)[C@@H]…`
CHEMBL4287199 ChEMBL	P00803	7.01 ~97.7 nM	898.9 Da LogP 1.38 TPSA 235.4	3 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N[C@@H](CCCN)C(=O)N(C)[…`
CHEMBL4279276 ChEMBL	P00803	6.98 ~104.7 nM	884.9 Da LogP 1.04 TPSA 244.2	3 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N[C@@H](CCCN)C(=O)N[C@H…`
CHEMBL4280386 ChEMBL	P00803	6.98 ~104.7 nM	870.9 Da LogP 0.65 TPSA 244.2	3 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N[C@@H](CCCN)C(=O)N[C@H…`
CHEMBL4290610 ChEMBL	P00803	6.97 ~107.2 nM	907.9 Da LogP 1.27 TPSA 246.8	3 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N[C@@H](Cc3cnc[nH]3)C(=…`
CHEMBL3924425 ChEMBL	P00803	6.96 ~109.6 nM	859.9 Da LogP 2.90 TPSA 236.2	2 viol.	✓ Clean	`CCCCc1ccc(-c2ccc(C(=O)N[C@@H](CCN)C(=O)N[C@H](C…`
CHEMBL4282334 ChEMBL	P00803	6.76 ~173.8 nM	885.9 Da LogP 1.51 TPSA 250.1	3 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N[C@@H](CCCN)C(=O)N[C@H…`
CHEMBL555725 ChEMBL	P00803	6.75 ~177.8 nM	215.2 Da LogP -0.18 TPSA 77.8	✓ Ro5	✓ Clean	`C[C@@H](O)[C@H]1C(=O)N2C(C(=O)O)=CS[C@@H]12`
CHEMBL4281328 ChEMBL	P00803	6.65 ~223.9 nM	924.9 Da LogP 1.99 TPSA 265.9	3 viol.	✓ Clean	`CCCCCCc1ccc(-c2c[nH]c3ccc(C(=O)N[C@@H](CCCN)C(=…`
CHEMBL3895001 ChEMBL	P00803	6.64 ~229.1 nM	736.7 Da LogP 0.33 TPSA 240.5	2 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N3CCC[C@H]3C(=O)N[C@H](…`
CHEMBL4291944 ChEMBL	P00803	6.64 ~229.1 nM	825.7 Da LogP -0.87 TPSA 250.1	3 viol.	✓ Clean	`C[C@@H]1NC(=O)[C@@H](NC(=O)[C@H](C)NC(=O)[C@@H]…`
CHEMBL4280228 ChEMBL	P00803	6.30 ~501.2 nM	902.9 Da LogP -0.00 TPSA 272.1	3 viol.	✓ Clean	`CCCCCCc1ccc(-n2cc(C(=O)N[C@@H](CCCN)C(=O)N[C@H]…`
CHEMBL141679 ChEMBL	P00803	6.07 ~851.1 nM	297.3 Da LogP 1.04 TPSA 72.9	✓ Ro5	✓ Clean	`C=CCOC(=O)C1=CS[C@H]2[C@@H]([C@@H](C)OC(C)=O)C(…`
CHEMBL138375 ChEMBL	P00803	6.04 ~912.0 nM	255.3 Da LogP 0.47 TPSA 66.8	✓ Ro5	✓ Clean	`C=CCOC(=O)C1=CS[C@H]2[C@@H]([C@@H](C)O)C(=O)N12`
CHEMBL1933111 ChEMBL	Q9M9Z2	—	1581.8 Da LogP 6.42 TPSA 421.5	4 viol.	✓ Clean	`CCOP(=O)(CCOCCOCCOCCOC(=O)NCc1cn(CCCCCNC(=O)CCC…`

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

No virtual-screening candidates for this protein.

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.

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A0A0H3GTU0

Chemistry

ChEMBL CHEMBL5410707 ChEMBL CHEMBL3947604 ChEMBL CHEMBL4284736 ChEMBL CHEMBL3922978 ChEMBL CHEMBL4283840 ChEMBL CHEMBL3934222 ChEMBL CHEMBL4283678 ChEMBL CHEMBL1784531 ChEMBL CHEMBL4282733 ChEMBL CHEMBL4291540 ChEMBL CHEMBL4291025 ChEMBL CHEMBL3957297 ChEMBL CHEMBL4294422 ChEMBL CHEMBL4292925 ChEMBL CHEMBL4287199 ChEMBL CHEMBL4279276 ChEMBL CHEMBL4280386 ChEMBL CHEMBL4290610 ChEMBL CHEMBL3924425 ChEMBL CHEMBL4282334 ChEMBL CHEMBL555725 ChEMBL CHEMBL4281328 ChEMBL CHEMBL3895001 ChEMBL CHEMBL4291944 ChEMBL CHEMBL4280228 ChEMBL CHEMBL141679 ChEMBL CHEMBL138375 ChEMBL CHEMBL1933111