KpKP13 Protein target profile

putative cystathionine-beta-synthase

Accession: KP13_31508

Gene: AHE42675.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H331

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Length 456

Pocket druggability (P2Rank · AlphaFold DB model) 0.936

Direct ligand evidence 0 56 total records

Functional annotation 0 EC 1 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

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Moderate predicted binding pocket FPocket selected-pocket score 0.57. This supports review but is not experimental validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.94. 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: Hit
Human identity (%): 54.255 Lower values reduce human off-target concern.
Human E-value: 7.6e-25
Gut microbiome similarity: 1.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT: 94.31 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) 0.936

Structure A0A0H3H331

Pocket Pocket 1

Druggability (FPocket) 0.574

Structure A0A0H3H331

Pocket Pocket 14

ColabFold model

P2Rank 0.956 · Pocket 1

FPocket 0.611 · Pocket 17

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 68 / 4744 genomes with a hit

Prevalence 1.4%

Sequence

Primary amino-acid sequence viewer.

MSLFHSVSDLIGHTPLLQLHKLDTGPCSLFLKLENQNPGGSIKDRVALSMINEAERQGKLAPGGTIIEATAGNTGLGLALIAAQKNYRLILVVPDKMSREKIFHLRALGATVLLTRSDVNKGHPAYYQDYARRLADETPGAFYIDQFNNDANPLAHATSTAPELYQQLEGDIDAIVVGVGSGGTLGGLQAWFAEHSPKTEFILADPAGSILADQVDTGRYGETGSWLVEGIGEDFIPPLARLEGVHTAYRVSDREAFHTARQLLQVEGVLAGSSTGTLLSAALRYCRAQSRPKRVVTFACDSGNKYLSKMFNDDWMRQQGLIARPEQGDLSDFIALRHDEGATVTAAPDDTLAAVFTRMRLYDISQLPVLEDGRVVGIVDEWDLIRHVQGDRQRFSLPVSEAMSRHVETLDKHAPESELQAILDRGLVAVIADNARFLGLVTRSDVLTAWRNRVAQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Subcellular localization

Localization: CytoplasmicMembrane

Gene Ontology (GO)

GO:0006535 OBSOLETE. The chemical reactions and pathways resulting in the formation of cysteine from L- serine.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

28 records

Show feature table

Start	End	DB	Term	Name
336	397	ProSiteProfiles	PS51371	CBS domain profile.
336	397	InterPro	IPR000644	CBS domain
11	307	Gene3D	G3DSA:3.40.50.1100	-
11	307	InterPro	IPR036052	Tryptophan synthase beta chain-like, PALP domain superfamily
3	320	SUPERFAMILY	SSF53686	Tryptophan synthase beta subunit-like PLP-dependent enzymes
3	320	InterPro	IPR036052	Tryptophan synthase beta chain-like, PALP domain superfamily
40	153	Gene3D	G3DSA:3.40.50.1100	-
40	153	InterPro	IPR036052	Tryptophan synthase beta chain-like, PALP domain superfamily
163	316	FunFam	G3DSA:3.40.50.1100:FF:000118	Related to CYS4-cystathionine beta-synthase
399	450	Pfam	PF00571	CBS domain
399	450	InterPro	IPR000644	CBS domain
344	388	Pfam	PF00571	CBS domain
344	388	InterPro	IPR000644	CBS domain
6	317	PANTHER	PTHR10314	CYSTATHIONINE BETA-SYNTHASE
8	301	Pfam	PF00291	Pyridoxal-phosphate dependent enzyme
8	301	InterPro	IPR001926	Tryptophan synthase beta chain-like, PALP domain
12	308	CDD	cd01561	CBS_like
322	455	Gene3D	G3DSA:3.10.580.10	-
322	455	InterPro	IPR046342	CBS domain superfamily
40	153	FunFam	G3DSA:3.40.50.1100:FF:000003	Cystathionine beta-synthase
32	50	ProSitePatterns	PS00901	Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site.
32	50	InterPro	IPR001216	Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site
343	452	SUPERFAMILY	SSF54631	CBS-domain pair
343	452	InterPro	IPR046342	CBS domain superfamily
332	449	CDD	cd04608	CBS_pair_CBS
332	449	InterPro	IPR046353	Cystathionine beta-synthase, C-terminal domain
342	389	SMART	SM00116	cbs_1
342	389	InterPro	IPR000644	CBS domain

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

0.936

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Surrounding area

Pocket 2 P2Rank #2

0.136

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Surrounding area

Pocket 3 P2Rank #3

0.09

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Surrounding area

Pocket 4 P2Rank #4

0.075

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Surrounding area

Pocket 5 P2Rank #5

0.048

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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 #14

0.574

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Surrounding area

Pocket 2 FPocket #6

0.384 Unusual size

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Surrounding area

Binding pockets · P2Rank

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

Pocket 1 P2Rank #1

0.956

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Surrounding area

Pocket 2 P2Rank #2

0.086

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Surrounding area

Pocket 3 P2Rank #3

0.063

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Surrounding area

Pocket 4 P2Rank #4

0.048

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Surrounding area

Pocket 5 P2Rank #5

0.046

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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_A0A0H3H331	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_31508	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.

56 records

Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records

Transferred evidence 6 records from similar proteins

Structural ligands 5 0 loaded crystals

Measured bioactivity 1 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

EVM PDB via homolog 333.2 Da · LogP -0.27 · TPSA 169.8 Open detail RCSB PDB

KOU PDB via homolog Detail RCSB PDB

P1T PDB via homolog Detail RCSB PDB

PE4 PDB via homolog Detail RCSB PDB

PMP PDB via homolog Detail RCSB PDB

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
EVM RCSB PDB	6C2Q	P32582	333.2 Da LogP -0.27 TPSA 169.8	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C-](CO)C(=O)O)O`
KOU RCSB PDB	3PC4	Q9VRD9	334.2 Da LogP -0.43 TPSA 169.8	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/C(CO)C(=O)O)O`
P1T RCSB PDB	6XYL	A0A125YSJ9	318.2 Da LogP 0.39 TPSA 149.2	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)CNC(=C)C(=O)O)O`
PE4 RCSB PDB	4COO	P35520	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
PMP RCSB PDB	6C4P	P32582	248.2 Da LogP 0.16 TPSA 125.9	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)CN)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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
AOA ChEMBL	P35520	6.00 ~1.0 µM	91.1 Da LogP -1.04 TPSA 72.5	✓ Ro5	✓ Clean	`C(C(=O)O)ON`

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
ZINC5650743 ZINC	1.000	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC6403917 ZINC	1.000	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC12501520 ZINC	0.688	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC3874716 ZINC	0.688	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769 ZINC	0.688	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548 ZINC	0.688	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829 ZINC	0.688	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830 ZINC	0.688	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5859031 ZINC	0.688	294.4 Da LogP 1.13 TPSA 55.4	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCC`
ZINC1532708 ZINC	0.660	248.2 Da LogP 0.16 TPSA 125.9	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(CN)c1O`
ZINC1532514 ZINC	0.646	247.1 Da LogP 0.52 TPSA 117.0	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(C=O)c1O`
ZINC2114966 ZINC	0.643	332.2 Da LogP 0.99 TPSA 149.5	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(/C=N/CCCC(=O)O)c1O`
ZINC1532705 ZINC	0.638	249.2 Da LogP 0.20 TPSA 120.1	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(CO)c1O`
ZINC1644613 ZINC	0.619	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`
ZINC1580161 ZINC	0.600	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118 ZINC	0.600	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257 ZINC	0.600	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654 ZINC	0.600	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44076059 ZINC	0.600	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101 ZINC	0.600	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5997860 ZINC	0.600	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC2555269 ZINC	0.591	220.3 Da LogP 1.22 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCOCCOCCOCCO`
ZINC4974293 ZINC	0.579	280.4 Da LogP 1.08 TPSA 55.4	✓ Ro5	✓ Clean	`CCOCCOCCOCOCCOCCOCC`
ZINC6824902 ZINC	0.576	401.2 Da LogP 3.22 TPSA 112.2	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(/C=N/c2ccccc2Br)c1O`
ZINC1656021 ZINC	0.574	233.2 Da LogP 1.01 TPSA 99.9	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(C)c1O`
ZINC100014200 ZINC	0.565	494.7 Da LogP 4.02 TPSA 84.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC100070166 ZINC	0.565	290.4 Da LogP 3.17 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCO`
ZINC100310628 ZINC	0.565	478.7 Da LogP 4.78 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC100365196 ZINC	0.565	302.5 Da LogP 4.71 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCO`
ZINC101772322 ZINC	0.565	434.7 Da LogP 4.76 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC103600921 ZINC	0.565	466.7 Da LogP 3.24 TPSA 84.8	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC14880431 ZINC	0.565	378.6 Da LogP 3.20 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC14881140 ZINC	0.565	306.4 Da LogP 2.41 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCOCCO`
ZINC16051619 ZINC	0.565	350.5 Da LogP 2.42 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCOCCOCCO`
ZINC2584424 ZINC	0.565	218.3 Da LogP 2.37 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCO`
ZINC4521877 ZINC	0.565	234.3 Da LogP 1.61 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCOCCOCCOCCO`
ZINC5273610 ZINC	0.565	322.4 Da LogP 1.64 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCOCCOCCOCCOCCOCCO`
ZINC58538366 ZINC	0.565	392.6 Da LogP 3.59 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC58631420 ZINC	0.565	422.6 Da LogP 3.22 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC59441819 ZINC	0.565	318.5 Da LogP 3.95 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCO`
ZINC59622400 ZINC	0.565	274.4 Da LogP 3.93 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCO`
ZINC71788551 ZINC	0.565	334.5 Da LogP 3.19 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCO`
ZINC71788564 ZINC	0.565	262.4 Da LogP 2.39 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCO`
ZINC71788567 ZINC	0.565	406.6 Da LogP 3.98 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC8214594 ZINC	0.565	362.6 Da LogP 3.97 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCO`
ZINC88260008 ZINC	0.565	390.6 Da LogP 4.75 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCO`
ZINC95784968 ZINC	0.565	450.7 Da LogP 4.00 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC95863931 ZINC	0.565	464.7 Da LogP 4.39 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC2527979 ZINC	0.564	296.3 Da LogP 0.32 TPSA 140.3	✓ Ro5	✓ Clean	`Cc1ncc(CO)c(/C=N/[C@@H](CCC(=O)O)C(=O)O)c1O`
ZINC2527980 ZINC	0.544	280.3 Da LogP 1.51 TPSA 103.0	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](/N=C/c1c(CO)cnc(C)c1O)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.

Cross-references

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

Sequence

UniProt A0A0H3H331

Chemistry

ChEMBL AOA