KpKP13 Protein target profile

FKBP-type 16 kDa peptidyl-prolyl cis-trans isomerase

Accession: KP13_01972

Gene: fkpB AHE46411.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GMC8
Length 149
Pocket druggability (P2Rank · AlphaFold DB model) 0.132
Direct ligand evidence 0 175 total records
Functional annotation 1 EC 1 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing 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 (%)
35.0 Lower values reduce human off-target concern.
Human E-value
1.38e-06
Gut microbiome similarity
2.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
51.773 Higher values support similarity to known essential genes.
DEG E-value
7.39e-49 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
81.9 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) 0.132
Structure A0A0H3GMC8
Pocket Pocket 1
Druggability (FPocket) 0.567
Structure A0A0H3GMC8
Pocket Pocket 1
ColabFold model
P2Rank 0.261 · Pocket 1
FPocket 0.468 · Pocket 8
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 124 / 4744 genomes with a hit
Prevalence 2.6%

Sequence

Primary amino-acid sequence viewer.

MSKSVQSNSAVLVHFTLKLDDGSTAESTRSNGKPALFRLGDTSLSEGLEQQLLGLKEGEKKAFSLEPDAAFGVPSPDLIQYFSRREFIDAGEPEIGAIMLFTAMDGSEMPGVIREVNGDSITVDFNHPLAGRTVHFDIEVLEIDPALEE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 1 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

1
  • GO:0003755 Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

10 records
Show feature table
Start End DB Term Name
13 142 Gene3D G3DSA:3.10.50.40 -
13 142 InterPro IPR046357 Peptidyl-prolyl cis-trans isomerase domain superfamily
73 129 FunFam G3DSA:2.40.10.330:FF:000002 Peptidyl-prolyl cis-trans isomerase
73 129 Gene3D G3DSA:2.40.10.330 -
3 149 PANTHER PTHR47861 FKBP-TYPE PEPTIDYL-PROLYL CIS-TRANS ISOMERASE SLYD
8 72 ProSiteProfiles PS50059 FKBP-type peptidyl-prolyl cis-trans isomerase domain profile.
8 72 InterPro IPR001179 FKBP-type peptidyl-prolyl cis-trans isomerase domain
5 143 SUPERFAMILY SSF54534 FKBP-like
5 141 Pfam PF00254 FKBP-type peptidyl-prolyl cis-trans isomerase
5 141 InterPro IPR001179 FKBP-type peptidyl-prolyl cis-trans isomerase 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
0.132
Likely same site as FPocket 7 1.4 Å 10 shared residues 100% of smaller site
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.567 Unusual size
Show in viewer
Surrounding area
Pocket 2 FPocket #7
0.236
Likely same site as P2Rank 1 1.4 Å 10 shared residues 100% of smaller site
Show in viewer
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_A0A0H3GMC8
AlphaFold DB full sequence Viewing
ColabFold KP13_01972
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.

175 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 125 records from similar proteins
Structural ligands 25 0 loaded crystals
Measured bioactivity 100 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
001 PDB via homolog 624.7 Da · LogP 6.54 · TPSA 87.2 Open detail RCSB PDB
587 PDB via homolog Detail RCSB PDB
60Z PDB via homolog Detail RCSB PDB
818 PDB via homolog Detail RCSB PDB
ARD PDB via homolog Detail RCSB PDB

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
001 RCSB PDB P62942 624.7 Da LogP 6.54 TPSA 87.2 2 viol. ✓ Clean COc1cc(cc(c1OC)OC)C(C(=O)N2CCCC[C@H]2C(=O)O[C@@…
587 RCSB PDB P62942 937.2 Da LogP 6.02 TPSA 192.5 3 viol. ✓ Clean CC[C@@H]1C=C([C@H]([C@@H](C[C@@H]([C@@H]2[C@H](…
60Z RCSB PDB P62942 609.8 Da LogP 5.16 TPSA 113.4 2 viol. ✓ Clean CC[C@H](Cc1ccccc1)[C@@H]2/C=C/C/C=C/C[C@H]([C@@…
818 RCSB PDB P62942 808.0 Da LogP 3.44 TPSA 198.6 2 viol. ✓ Clean CC[C@@H]1\C=C(\[C@H]([C@@H](C[C@@H]([C@@H]2[C@H…
ARD RCSB PDB P62942 980.3 Da LogP 8.32 TPSA 186.2 3 viol. ✓ Clean Cc1ccc(s1)[C@@H]/2C[C@@H]3CC[C@H]([C@@](O3)(C(=…
BTB RCSB PDB Q5SLE7 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
BUQ RCSB PDB P62942 88.1 Da LogP -0.04 TPSA 37.3 ✓ Ro5 ✓ Clean CC(=O)CCO
DSS RCSB PDB P62942 124.2 Da LogP 0.69 TPSA 17.1 ✓ Ro5 ✓ Clean CSC[S@@](=O)C
FK5 RCSB PDB P18203 804.0 Da LogP 4.64 TPSA 178.4 2 viol. ✓ Clean C[C@@H]1C[C@@H]([C@@H]2[C@H](C[C@H]([C@@](O2)(C…
FKA RCSB PDB P62942 941.2 Da LogP 5.38 TPSA 216.7 3 viol. ✓ Clean C[C@@H]1C[C@@H]([C@@H]2[C@H](C[C@H]([C@@](O2)(C…
MLA RCSB PDB P62942 104.1 Da LogP -0.45 TPSA 74.6 ✓ Ro5 ✓ Clean C(C(=O)O)C(=O)O
MR8 RCSB PDB P62942 928.2 Da LogP 6.83 TPSA 184.4 3 viol. ✓ Clean C[C@@H]1CC[C@H]2C[C@@H](/C(=C/C=C/C=C/[C@H](C[C…
MYR RCSB PDB P18203 228.4 Da LogP 4.77 TPSA 37.3 ✓ Ro5 ✓ Clean CCCCCCCCCCCCCC(=O)O
NH4 RCSB PDB P62942 18.0 Da LogP 0.38 TPSA 36.5 ✓ Ro5 ✓ Clean [NH4+]
OOZ RCSB PDB P62942 778.0 Da LogP 3.82 TPSA 189.4 2 viol. ✓ Clean CC[C@@H]1/C=C(/C[C@@H](C[C@@H]([C@@H]2[C@H](C[C…
OP5 RCSB PDB P62942 820.0 Da LogP 4.04 TPSA 195.4 2 viol. ✓ Clean C[C@@H]1C[C@@H]([C@@H]2[C@H](C[C@H]([C@@](O2)(C…
OP8 RCSB PDB P62942 808.0 Da LogP 3.68 TPSA 190.9 2 viol. ✓ Clean CC[C@@H]1[C@@H]2[C@](O2)(C[C@@H](C[C@@H]([C@@H]…
PE8 RCSB PDB P62942 370.4 Da LogP -0.91 TPSA 105.1 ✓ Ro5 ✓ Clean C(COCCOCCOCCOCCOCCOCCOCCO)O
R27 RCSB PDB P62942 860.1 Da LogP 4.56 TPSA 202.7 2 viol. ✓ Clean C[C@@H]1C[C@@H]([C@@H]2[C@H](C[C@H]([C@@](O2)(C…
RAP RCSB PDB P62942 914.2 Da LogP 6.18 TPSA 195.4 3 viol. ✓ Clean C[C@@H]1CC[C@H]2C[C@@H](C(=CC=C\C=C\[C@H](C[C@H…
SB1 RCSB PDB P62942 437.6 Da LogP 3.96 TPSA 90.0 ✓ Ro5 ✓ Clean CC1(COC(=O)CCCCCCCCCCCOC(=O)[C@@H]2CCCCN2C(=O)C…
SB3 RCSB PDB P62942 449.6 Da LogP 5.29 TPSA 63.7 1 viol. ✓ Clean CCC(C)(C)C(=O)C(=O)N1CCCC[C@H]1C(=O)OC(CCc2cccc…
SBX RCSB PDB P62942 455.6 Da LogP 5.50 TPSA 63.7 1 viol. ✓ Clean CCC(C)(C)C(=O)C(=O)N1CCCC[C@H]1C(=O)OC(CCc2cccc…
SUB RCSB PDB P62942 476.6 Da LogP 2.39 TPSA 92.8 ✓ Ro5 ✓ Clean CCOC(=O)C(Cc1ccccc1)NC(=O)[C@@H]2CSCC[N@]2S(=O)…
TST RCSB PDB P62942 414.5 Da LogP 1.72 TPSA 103.8 ✓ Ro5 ✓ Clean Cc1ccc(cc1)S(=O)(=O)N2CCSC[C@H]2C(=O)N[C@@H](CC…

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.

Chemistry

ChEMBL GPI ChEMBL CHEMBL5634031 ChEMBL CHEMBL413 ChEMBL CHEMBL5935211 ChEMBL CHEMBL5275279 ChEMBL CHEMBL4449096 ChEMBL CHEMBL6063426 ChEMBL CHEMBL262778 ChEMBL CHEMBL4090599 ChEMBL CHEMBL151727 ChEMBL CHEMBL5934171 ChEMBL CHEMBL52035 ChEMBL CHEMBL5758552 ChEMBL CHEMBL5765262 ChEMBL CHEMBL5819479 ChEMBL CHEMBL5822423 ChEMBL CHEMBL5835485 ChEMBL CHEMBL5838984 ChEMBL CHEMBL5853787 ChEMBL CHEMBL5866833 ChEMBL CHEMBL5877457 ChEMBL CHEMBL5891210 ChEMBL CHEMBL5897947 ChEMBL CHEMBL5926284 ChEMBL CHEMBL5948930 ChEMBL CHEMBL5984129 ChEMBL CHEMBL5986579 ChEMBL CHEMBL5994752 ChEMBL CHEMBL2052020 ChEMBL CHEMBL303852 ChEMBL CHEMBL71458 ChEMBL CHEMBL68027 ChEMBL CHEMBL5782802 ChEMBL CHEMBL151841 ChEMBL CHEMBL33094 ChEMBL CHEMBL4276944 ChEMBL CHEMBL4280369 ChEMBL CHEMBL4287849 ChEMBL CHEMBL4291011 ChEMBL CHEMBL4291053 ChEMBL CHEMBL54189 ChEMBL CHEMBL5763714 ChEMBL CHEMBL280262 ChEMBL CHEMBL4279943 ChEMBL CHEMBL5757904 ChEMBL CHEMBL70822 ChEMBL CHEMBL8597 ChEMBL AP1 ChEMBL CHEMBL48863 ChEMBL CHEMBL50795 ChEMBL CHEMBL437064 ChEMBL CHEMBL263776 ChEMBL CHEMBL170544 ChEMBL CHEMBL303180 ChEMBL CHEMBL312157 ChEMBL CHEMBL299136 ChEMBL CHEMBL150120 ChEMBL CHEMBL2058796 ChEMBL CHEMBL300752 ChEMBL CHEMBL423033 ChEMBL CHEMBL4281041 ChEMBL CHEMBL295372 ChEMBL CHEMBL432484 ChEMBL CHEMBL140442 ChEMBL CHEMBL405104 ChEMBL RAD ChEMBL CHEMBL419817 ChEMBL CHEMBL216404 ChEMBL CHEMBL266848 ChEMBL CHEMBL5218737 ChEMBL CHEMBL51516 ChEMBL CHEMBL5220794 ChEMBL CHEMBL5913279 ChEMBL CHEMBL277083 ChEMBL CHEMBL4283828 ChEMBL CHEMBL368142 ChEMBL CHEMBL5903622 ChEMBL CHEMBL109950 ChEMBL CHEMBL2062149 ChEMBL CHEMBL326881 ChEMBL CHEMBL417192 ChEMBL CHEMBL4279511 ChEMBL CHEMBL431360 ChEMBL CHEMBL293155 ChEMBL CHEMBL320478 ChEMBL CHEMBL266912 ChEMBL CHEMBL277560 ChEMBL CHEMBL435906 ChEMBL DWT ChEMBL CHEMBL5218786 ChEMBL CHEMBL5830362 ChEMBL CHEMBL118937 ChEMBL CHEMBL4283415 ChEMBL CHEMBL170655 ChEMBL CHEMBL5219513 ChEMBL CHEMBL5796581 ChEMBL CHEMBL355620 ChEMBL CHEMBL4084630 ChEMBL CHEMBL4102121 ChEMBL RRZ