KpKP13 Protein target profile

Peptidyl-prolyl cis-trans isomerase A

Accession: KP13_00717

Gene: ppiA AHE42335.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GWQ5
Length 189
Pocket druggability (P2Rank · AlphaFold DB model) 0.166
Direct ligand evidence 0 190 total records
Functional annotation 1 EC 4 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 (%)
44.231 Lower values reduce human off-target concern.
Human E-value
2.78e-09
Gut microbiome similarity
7.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
55.901 Higher values support similarity to known essential genes.
DEG E-value
5.24e-62 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
92.14 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) 0.166
Structure A0A0H3GWQ5
Pocket Pocket 1
Druggability (FPocket) 0.631
Structure A0A0H3GWQ5
Pocket Pocket 2
ColabFold model
P2Rank 0.141 · Pocket 1
FPocket 0.199 · Pocket 2
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 334 / 4744 genomes with a hit
Prevalence 7.0%

Sequence

Primary amino-acid sequence viewer.

MLKSTLAAMAAVFAISAFSPAMAAKGDPHVLLTTSAGNIELELNSQKAPISVDNFLKYVNSGFYNNTTFHRVIPGFMVQGGGFNEQMQQKQPNPPIKNEADNGLRNTRGTIAMARTADQDSATSQFFINVADNAFLDHGQRDFGYAVFGKVVKGMDVADKISQVQTHNVGPYQNVPTKPVVILSAKVLP

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Subcellular localization

Localization
Periplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0000413 The modification of a protein by cis-trans isomerization of a proline residue.
  • GO:0003755 Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
  • GO:0006457 The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
  • GO:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

27 records
Show feature table
Start End DB Term Name
24 189 Gene3D G3DSA:2.40.100.10 -
24 189 InterPro IPR029000 Cyclophilin-like domain superfamily
1 23 SignalP_EUK SignalP-noTM SignalP-noTM
1 5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
24 189 FunFam G3DSA:2.40.100.10:FF:000006 Peptidyl-prolyl cis-trans isomerase
24 187 PANTHER PTHR43246 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE CYP38, CHLOROPLASTIC
24 187 InterPro IPR044665 Cyclophilin-type peptidyl-prolyl cis-trans isomerase, E. coli cyclophilin A-like
30 187 Pfam PF00160 Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
30 187 InterPro IPR002130 Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain
64 81 ProSitePatterns PS00170 Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature.
64 81 InterPro IPR020892 Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site
1 23 Phobius SIGNAL_PEPTIDE Signal peptide region
1 23 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
34 187 ProSiteProfiles PS50072 Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile.
34 187 InterPro IPR002130 Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain
31 185 CDD cd01920 cyclophilin_EcCYP_like
24 189 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
25 188 SUPERFAMILY SSF50891 Cyclophilin-like
25 188 InterPro IPR029000 Cyclophilin-like domain superfamily
19 23 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
69 81 PRINTS PR00153 Cyclophilin peptidyl-prolyl cis-trans isomerase signature
69 81 InterPro IPR002130 Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain
43 58 PRINTS PR00153 Cyclophilin peptidyl-prolyl cis-trans isomerase signature
43 58 InterPro IPR002130 Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain
143 158 PRINTS PR00153 Cyclophilin peptidyl-prolyl cis-trans isomerase signature
143 158 InterPro IPR002130 Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain
6 18 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.

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
0.166
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.006
Likely same site as FPocket 2 1.0 Å 7 shared residues 88% 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 #2
0.631
Likely same site as P2Rank 2 1.0 Å 7 shared residues 88% 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_A0A0H3GWQ5
AlphaFold DB full sequence Viewing
ColabFold KP13_00717
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.

190 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 140 records from similar proteins
Structural ligands 40 0 loaded crystals
Measured bioactivity 100 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
76X PDB via homolog 109.1 Da · LogP 0.25 · TPSA 64.9 Open detail RCSB PDB
78E PDB via homolog Detail RCSB PDB
78R PDB via homolog Detail RCSB PDB
78X PDB via homolog Detail RCSB PDB
7HG 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
76X RCSB PDB P62937 109.1 Da LogP 0.25 TPSA 64.9 ✓ Ro5 ✓ Clean c1cc(c(nc1)N)N
78E RCSB PDB P62937 554.7 Da LogP 2.68 TPSA 137.1 1 viol. ✓ Clean CC(C)[C@H]1C(=O)N[C@H](C(=O)N2CCC[C@H](N2)C(=O)…
78R RCSB PDB P62937 634.8 Da LogP 3.26 TPSA 146.3 1 viol. ✓ Clean C[C@@H]1[C@@H](CC/C=C/c2cccc(c2)COC(=O)[C@@H]3C…
78X RCSB PDB P62937 648.8 Da LogP 3.82 TPSA 146.3 1 viol. ✓ Clean C[C@@H]1c2cccc(c2)/C=C/CC[C@H]([C@H](C(=O)N[C@H…
7HG RCSB PDB P62937 642.8 Da LogP 2.42 TPSA 155.5 1 viol. ✓ Clean C[C@H]1[C@H](/C=C/C=C/CCOC(=O)[C@@H]2CCCN(N2)C(…
838 RCSB PDB P62937 556.7 Da LogP 2.89 TPSA 126.1 1 viol. ✓ Clean C[C@@H]1c2cccc(c2)/C=C/CC[C@H]([C@H](C(=O)N[C@H…
92Z RCSB PDB P62937 110.1 Da LogP -0.17 TPSA 55.5 ✓ Ro5 ✓ Clean C1C=C(C(=O)N=C1)N
938 RCSB PDB P62937 129.6 Da LogP 0.71 TPSA 51.8 ✓ Ro5 ✓ Clean c1c(c(ncn1)Cl)N
93B RCSB PDB P62937 116.2 Da LogP -0.15 TPSA 24.1 ✓ Ro5 ✓ Clean C1CNC(=S)NC1
93E RCSB PDB P62937 128.6 Da LogP 1.32 TPSA 38.9 ✓ Ro5 ✓ Clean c1cc(c(nc1)N)Cl
93K RCSB PDB P62937 151.2 Da LogP -0.05 TPSA 95.1 ✓ Ro5 ✓ Clean c1cc(c(cc1C(=O)N)N)N
93Q RCSB PDB P62937 108.1 Da LogP 0.97 TPSA 38.9 ✓ Ro5 ✓ Clean Cc1cccnc1N
EA4 RCSB PDB P62937 251.3 Da LogP 0.63 TPSA 93.4 ✓ Ro5 Alert CCOC(=O)CNC(=O)NCc1ccc(cc1)N
F0Q RCSB PDB P62937 527.4 Da LogP 2.63 TPSA 122.3 1 viol. Alert Cn1nc(nn1)CN(Cc2ccc(cc2)N)C(=O)NCC(=O)N3CCC[C@@…
F0T RCSB PDB P62937 305.4 Da LogP 1.75 TPSA 84.7 ✓ Ro5 Alert CCOC(=O)CNC(=O)N(Cc1ccc(cc1)N)CC2CC2
F0W RCSB PDB P62937 347.4 Da LogP 0.07 TPSA 128.3 ✓ Ro5 Alert CCOC(=O)CNC(=O)N(Cc1ccc(cc1)N)Cc2nnn(n2)C
F1E RCSB PDB P62937 346.4 Da LogP 0.67 TPSA 115.4 ✓ Ro5 Alert CCOC(=O)CNC(=O)N(Cc1ccc(cc1)N)Cc2cn(nn2)C
F1Q RCSB PDB P62937 333.4 Da LogP 0.06 TPSA 139.1 ✓ Ro5 Alert CCOC(=O)CNC(=O)N(Cc1ccc(cc1)N)Cc2[nH]nnn2
F1Z RCSB PDB P62937 289.3 Da LogP 0.98 TPSA 84.7 ✓ Ro5 Alert CCOC(=O)CNC(=O)N(CC#C)Cc1ccc(cc1)N
L36 RCSB PDB P62937 293.4 Da LogP 1.75 TPSA 84.7 ✓ Ro5 Alert CCCN(Cc1ccc(cc1)N)C(=O)NCC(=O)OCC
L60 RCSB PDB P62937 100.1 Da LogP -0.31 TPSA 41.1 ✓ Ro5 ✓ Clean C1CNC(=O)NC1
L89 RCSB PDB P62937 109.1 Da LogP 0.25 TPSA 64.9 ✓ Ro5 ✓ Clean c1cncc(c1N)N
L97 RCSB PDB P62937 128.6 Da LogP 1.32 TPSA 38.9 ✓ Ro5 ✓ Clean c1cc(c(nc1)Cl)N
L99 RCSB PDB P62937 166.2 Da LogP -0.55 TPSA 107.2 ✓ Ro5 ✓ Clean c1cc(c(cc1C(=O)NN)N)N
LSA RCSB PDB P62937 183.2 Da LogP 0.12 TPSA 63.2 ✓ Ro5 ✓ Clean c1ccc2c(c1)C(=O)NS2(=O)=O
ME2 RCSB PDB A5YBL8 148.2 Da LogP 0.69 TPSA 27.7 ✓ Ro5 ✓ Clean CCOCCOCCOC
PG5 RCSB PDB Q8SRE1 178.2 Da LogP 0.31 TPSA 36.9 ✓ Ro5 ✓ Clean COCCOCCOCCOC
SFA RCSB PDB P62937 1090.4 Da LogP 5.41 TPSA 273.4 4 viol. ✓ Clean CC[C@H]1C[C@@H]([C@@]2([C@H]([C@H]([C@H]([C@@H]…
SFM RCSB PDB P62937 740.9 Da LogP 1.77 TPSA 214.8 3 viol. ✓ Clean C[C@H]1[C@H](/C=C/C=C/C[C@H](OC(=O)[C@@H]2CCCN(…
UMM RCSB PDB P62937 546.7 Da LogP 2.47 TPSA 135.3 1 viol. ✓ Clean CC(C)[C@@H](C(=O)N[C@H]1Cc2cccc(c2)OCCCCOC(=O)[…
UNU RCSB PDB P62937 121.1 Da LogP 0.79 TPSA 43.1 ✓ Ro5 ✓ Clean c1ccc(cc1)C(=O)N
UO7 RCSB PDB P62937 521.6 Da LogP 2.40 TPSA 129.7 1 viol. ✓ Clean C[C@@H]1c2ccc3cnc(cc3c2)/C=C/CC(=O)N[C@H](C(=O)…
UOD RCSB PDB P62937 549.7 Da LogP 3.03 TPSA 129.7 1 viol. ✓ Clean C[C@@H]1c2ccc3ccc(cc3n2)/C=C/C(C(=O)N[C@H](C(=O…
UOG RCSB PDB P62937 549.7 Da LogP 3.03 TPSA 129.7 1 viol. ✓ Clean C[C@@H]1c2ccc3ccc(cc3n2)/C=C/C(C(=O)O[C@H](C(=O…
UOJ RCSB PDB P62937 561.7 Da LogP 3.18 TPSA 129.7 1 viol. ✓ Clean C[C@@H]1c2ccc3ccc(cc3n2)/C=C/C(C(=O)O[C@H](C(=O…
WM1 RCSB PDB P62937 122.1 Da LogP 0.18 TPSA 56.0 ✓ Ro5 ✓ Clean c1ccnc(c1)C(=O)N
WM2 RCSB PDB P62937 127.2 Da LogP 1.05 TPSA 43.1 ✓ Ro5 ✓ Clean C1CCC(CC1)C(=O)N
WM3 RCSB PDB P62937 172.2 Da LogP -0.16 TPSA 72.2 ✓ Ro5 ✓ Clean c1ccc(cc1)S(=O)(=O)NN
WM4 RCSB PDB P62937 136.2 Da LogP 0.29 TPSA 55.1 ✓ Ro5 ✓ Clean c1ccc(cc1)C(=O)NN
ZXX RCSB PDB P62937 448.5 Da LogP 0.25 TPSA 137.1 ✓ Ro5 ✓ Clean CC(C)[C@@H](C(=O)N[C@@H](Cc1cccc(c1)O)C(=O)N2CC…

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 CHEMBL3704747 ChEMBL CHEMBL3344493 ChEMBL CHEMBL5759368 ChEMBL CHEMBL5792144 ChEMBL CHEMBL5812164 ChEMBL CHEMBL6051666 ChEMBL CHEMBL3344501 ChEMBL CHEMBL5791301 ChEMBL CHEMBL5810211 ChEMBL CHEMBL5856868 ChEMBL CHEMBL5942857 ChEMBL CHEMBL5994784 ChEMBL CHEMBL6010886 ChEMBL CHEMBL6059588 ChEMBL CHEMBL6062788 ChEMBL CHEMBL5757514 ChEMBL CHEMBL5866658 ChEMBL CHEMBL6003202 ChEMBL CHEMBL6026994 ChEMBL CHEMBL6056488 ChEMBL CHEMBL5842028 ChEMBL CHEMBL3704745 ChEMBL CHEMBL5741417 ChEMBL CHEMBL5831563 ChEMBL CHEMBL5842043 ChEMBL CHEMBL6048373 ChEMBL CHEMBL3344496 ChEMBL CHEMBL5812196 ChEMBL CHEMBL5867542 ChEMBL CHEMBL5967576 ChEMBL CHEMBL5976250 ChEMBL CHEMBL5985508 ChEMBL CHEMBL5992700 ChEMBL CHEMBL6023421 ChEMBL CHEMBL6038296 ChEMBL CHEMBL6044098 ChEMBL CHEMBL6058387 ChEMBL CHEMBL1651956 ChEMBL CHEMBL5798116 ChEMBL CHEMBL5821248 ChEMBL CHEMBL5974662 ChEMBL CHEMBL6062808 ChEMBL CHEMBL3220760 ChEMBL CHEMBL3344502 ChEMBL CHEMBL3344503 ChEMBL CHEMBL5859080 ChEMBL CHEMBL5960352 ChEMBL CHEMBL6018548 ChEMBL CHEMBL6023618 ChEMBL CHEMBL5744117 ChEMBL CHEMBL5926312 ChEMBL CHEMBL3344499 ChEMBL CHEMBL5820903 ChEMBL CHEMBL5877920 ChEMBL CHEMBL5887631 ChEMBL CHEMBL5904243 ChEMBL CHEMBL6037963 ChEMBL CHEMBL6061966 ChEMBL CHEMBL5740960 ChEMBL CHEMBL5757253 ChEMBL CHEMBL5962188 ChEMBL CHEMBL5981471 ChEMBL CHEMBL6043586 ChEMBL CHEMBL3344494 ChEMBL CHEMBL559525 ChEMBL CHEMBL5739566 ChEMBL CHEMBL5850260 ChEMBL CHEMBL5873894 ChEMBL CHEMBL5902225 ChEMBL CHEMBL5906552 ChEMBL CHEMBL5922149 ChEMBL CHEMBL5988852 ChEMBL CHEMBL5788636 ChEMBL CHEMBL6046692 ChEMBL CHEMBL6050788 ChEMBL CHEMBL3344500 ChEMBL CHEMBL5816255 ChEMBL CHEMBL5887073 ChEMBL CHEMBL5971933 ChEMBL CHEMBL5983054 ChEMBL CHEMBL6000275 ChEMBL CHEMBL5840800 ChEMBL CHEMBL5962940 ChEMBL CHEMBL6047322 ChEMBL CHEMBL6060257 ChEMBL CHEMBL5880006 ChEMBL CHEMBL5813010 ChEMBL CHEMBL5826107 ChEMBL CHEMBL5848922 ChEMBL CHEMBL5964648 ChEMBL CHEMBL6031839 ChEMBL CHEMBL6018012 ChEMBL CHEMBL2375162 ChEMBL CHEMBL5942804 ChEMBL CHEMBL3220746 ChEMBL CHEMBL3344498 ChEMBL CHEMBL3704746 ChEMBL CHEMBL5843757 ChEMBL CHEMBL559858 ChEMBL CHEMBL5795040