KpKP13 Protein target profile

Beta-lactamase TEM1

Accession: KP13_01391

Gene: AHE47439.1 3D evidence: Experimental + ColabFold model UniProt Q9R435
Length 286
Pocket druggability (P2Rank · Experimental) 0.172
Direct ligand evidence 0 194 total records
Functional annotation 1 EC 4 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.

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
0.5% 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
94.29 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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) 0.172
Structure 1HTZ
Pocket Pocket 1
Druggability (FPocket) 0.408
Structure 1HTZ
Pocket Pocket 2
ColabFold model
P2Rank 0.27 · Pocket 1
FPocket 0.146 · Pocket 2
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 24 / 4744 genomes with a hit
Prevalence 0.5%

Sequence

Primary amino-acid sequence viewer.

MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW

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:0008800 Catalysis of the reaction: a beta-lactam + H2O = a substituted beta-amino acid.
  • GO:0017001 The chemical reactions and pathways resulting in the breakdown of antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
  • GO:0046677 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
  • GO:0030655 The chemical reactions and pathways resulting in the breakdown of a beta-lactam antibiotic, any member of a class of natural or semisynthetic antibiotics whose characteristic feature is a strained, four-membered beta-lactam ring. They include the penicillins and many of the cephalosporins.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

31 records
Show feature table
Start End DB Term Name
29 285 SUPERFAMILY SSF56601 beta-lactamase/transpeptidase-like
29 285 InterPro IPR012338 Beta-lactamase/transpeptidase-like
25 286 Gene3D G3DSA:3.40.710.10 -
25 286 InterPro IPR012338 Beta-lactamase/transpeptidase-like
1 7 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
24 286 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 23 Phobius SIGNAL_PEPTIDE Signal peptide region
20 23 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 23 SignalP_EUK SignalP-noTM SignalP-noTM
64 79 ProSitePatterns PS00146 Beta-lactamase class-A active site.
64 79 InterPro IPR023650 Beta-lactamase, class-A active site
48 261 Pfam PF13354 Beta-lactamase enzyme family
48 261 InterPro IPR045155 Beta-lactamase class A, catalytic domain
62 79 PRINTS PR00118 Beta-lactamase class A signature
62 79 InterPro IPR000871 Beta-lactamase, class-A
219 234 PRINTS PR00118 Beta-lactamase class A signature
219 234 InterPro IPR000871 Beta-lactamase, class-A
140 164 PRINTS PR00118 Beta-lactamase class A signature
140 164 InterPro IPR000871 Beta-lactamase, class-A
166 191 PRINTS PR00118 Beta-lactamase class A signature
166 191 InterPro IPR000871 Beta-lactamase, class-A
30 54 PRINTS PR00118 Beta-lactamase class A signature
30 54 InterPro IPR000871 Beta-lactamase, class-A
104 129 PRINTS PR00118 Beta-lactamase class A signature
104 129 InterPro IPR000871 Beta-lactamase, class-A
202 217 PRINTS PR00118 Beta-lactamase class A signature
202 217 InterPro IPR000871 Beta-lactamase, class-A
33 286 PANTHER PTHR35333 BETA-LACTAMASE
33 286 InterPro IPR000871 Beta-lactamase, class-A
1 25 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
8 19 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
0.172
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
0.408
Show in viewer
Surrounding area
Pocket 2 FPocket #3
0.384
Show in viewer
Surrounding area
All structural evidence 1 experimental · 1 predicted

Structural evidence

1 + 1

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
PDB 1HTZ
X-ray 2.40 Å A,B,C,D,E,F
92.0% 24-286
Viewing
ColabFold KP13_01391
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.

194 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 144 records from similar proteins
Structural ligands 44 0 loaded crystals
Measured bioactivity 100 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
0RJ PDB via homolog 132.1 Da · LogP -1.86 · TPSA 92.4 Open detail RCSB PDB
105 PDB via homolog Detail RCSB PDB
17K PDB via homolog Detail RCSB PDB
17O PDB via homolog Detail RCSB PDB
1OG 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
0RJ RCSB PDB P0AD64 132.1 Da LogP -1.86 TPSA 92.4 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)N)NC=O
105 RCSB PDB P62593 294.5 Da LogP 1.05 TPSA 95.6 ✓ Ro5 ✓ Clean B(CNC(=O)c1c(onc1c2ccccc2Cl)C)(O)O
17K RCSB PDB P0AD64 458.5 Da LogP 2.38 TPSA 134.4 ✓ Ro5 ✓ Clean C[C@](COC(=O)Cc1ccccc1)([C@H](C(=O)O)Nc2c(cc3n2…
17O RCSB PDB P0AD64 309.4 Da LogP 1.47 TPSA 84.2 ✓ Ro5 ✓ Clean c1c2n(nc1C3C(=CNC(=CS3)C(=O)O)C=O)CSC2
1OG RCSB PDB P0AD64 403.4 Da LogP -0.09 TPSA 153.5 ✓ Ro5 ✓ Clean CC(=O)OC/C/1=C(/N=C\[C@H]([C@@H](S(=O)(=O)C1)C(…
2AW RCSB PDB P0AD64 381.4 Da LogP -0.21 TPSA 167.3 ✓ Ro5 ✓ Clean C[C@](COC(=O)CCCCC(=O)O)([C@H](C(=O)O)NCCC=O)S(…
2UL RCSB PDB Q79DR3 342.2 Da LogP 0.12 TPSA 132.9 ✓ Ro5 ✓ Clean B([C@H](Cc1cccc(c1)C(=O)O)NC(=O)[C@@H](c2ccccc2…
3GE RCSB PDB P0AD64 265.3 Da LogP -0.90 TPSA 123.9 ✓ Ro5 ✓ Clean CC(C)([C@H](C(=O)O)N/C=C(\CO)/C=O)S(=O)O
AKR RCSB PDB P0AD64 72.1 Da LogP 0.26 TPSA 37.3 ✓ Ro5 ✓ Clean C=CC(=O)O
ALP RCSB PDB P62593 249.3 Da LogP -0.43 TPSA 106.9 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@H](CO)C(=O)O)C(=O)O)C
BJH RCSB PDB P62593 267.0 Da LogP -0.85 TPSA 127.1 ✓ Ro5 ✓ Clean B([C@H](Cc1cccc(c1O)C(=O)O)NC(=O)C)(O)O
BJI RCSB PDB P62593 251.0 Da LogP -0.56 TPSA 106.9 ✓ Ro5 ✓ Clean B([C@H](Cc1cccc(c1)C(=O)O)NC(=O)C)(O)O
BJP RCSB PDB P62593 327.1 Da LogP 0.67 TPSA 106.9 ✓ Ro5 ✓ Clean B([C@H](Cc1cccc(c1)C(=O)O)NC(=O)Cc2ccccc2)(O)O
CB4 RCSB PDB P62593 330.1 Da LogP -1.56 TPSA 167.4 ✓ Ro5 ✓ Clean B(CNC(=O)C(=NOC(C)(C)C(=O)O)c1csc(n1)N)(O)O
CBT RCSB PDB P62593 334.2 Da LogP 3.71 TPSA 57.7 ✓ Ro5 ✓ Clean c1cc(ccc1CN(Cc2ccc(cc2)Cl)c3n[nH]nn3)Cl
CXB RCSB PDB P62593 258.1 Da LogP -1.80 TPSA 130.1 ✓ Ro5 ✓ Clean B(CNC(=O)/C(=N\OC)/c1csc(n1)N)(O)O
CZ6 RCSB PDB P0AD64 412.3 Da LogP 1.06 TPSA 145.4 ✓ Ro5 ✓ Clean B1(O[C@H](CC(O1)(C)C)C)CNC(=O)/C(=N\OC(C)(C)C(=…
CZ7 RCSB PDB P0AD64 390.2 Da LogP -1.84 TPSA 162.9 ✓ Ro5 ✓ Clean B(CNC(=O)[C@@H](c1ccc(cc1)O)NC(=O)N2C=CN(C(=O)C…
CZ8 RCSB PDB P0AD64 420.2 Da LogP -1.78 TPSA 159.5 ✓ Ro5 ✓ Clean B(CNC(=O)[C@@H](CCc1ccc(cc1)O)NC(=O)N2CCN(C(=O)…
CZ9 RCSB PDB P0AD64 406.2 Da LogP -2.17 TPSA 159.5 ✓ Ro5 ✓ Clean B(CNC(=O)[C@@H](Cc1ccc(cc1)O)NC(=O)N2CCN(C(=O)C…
ESA RCSB PDB P0AD64 110.1 Da LogP -0.11 TPSA 54.4 ✓ Ro5 ✓ Clean CCS(=O)(=O)O
FLC RCSB PDB P62593 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
FOS RCSB PDB P62593 245.2 Da LogP 1.05 TPSA 95.9 ✓ Ro5 ✓ Clean c1ccc(cc1)COC(=O)NCP(=O)(O)O
FTA RCSB PDB P62593 303.3 Da LogP 2.92 TPSA 102.3 ✓ Ro5 Alert c1ccc(cc1)Nc2ccc(cc2)NC=C(C#N)c3n[nH]nn3
IM2 RCSB PDB P62593 301.4 Da LogP -0.23 TPSA 122.5 ✓ Ro5 ✓ Clean [H]/N=C/NCCSC1=C(N[C@H](C1)[C@H](C=O)[C@@H](C)O…
LN1 RCSB PDB P0AD64 490.5 Da LogP 1.79 TPSA 174.9 ✓ Ro5 Alert C[C@](COC(=O)Cc1ccc(c(c1)O)O)([C@H](C(=O)O)Nc2c…
MA4 RCSB PDB P30896 508.6 Da LogP -0.84 TPSA 178.5 3 viol. ✓ Clean C1CCC(CC1)CCCCCCO[C@H]2[C@@H]([C@H]([C@@H]([C@H…
MDD RCSB PDB P0AD64 72.1 Da LogP -0.23 TPSA 34.1 ✓ Ro5 ✓ Clean C(C=O)C=O
MER RCSB PDB P0AD64 385.5 Da LogP -0.36 TPSA 119.0 ✓ Ro5 ✓ Clean C[C@@H]1[C@@H](NC(=C1S[C@H]2C[C@H](NC2)C(=O)N(C…
MXF RCSB PDB P0AD64 426.5 Da LogP 0.28 TPSA 172.5 ✓ Ro5 ✓ Clean C[C@](COC(=O)NCCN)([C@H](C(=O)O)Nc1c(cc2n1cccc2…
NBF RCSB PDB P62593 273.1 Da LogP 0.98 TPSA 78.8 ✓ Ro5 ✓ Clean B(CNC(=O)c1c2ccccc2ccc1OCC)(O)O
NXL RCSB PDB P0AD64 267.3 Da LogP -2.21 TPSA 139.0 ✓ Ro5 ✓ Clean C1C[C@H](N(C[C@@H]1NOS(=O)(=O)O)C=O)C(=O)N
PNM RCSB PDB P62593 336.4 Da LogP 0.81 TPSA 95.5 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)Cc2ccccc2…
SA2 RCSB PDB P0AD64 365.4 Da LogP -0.48 TPSA 167.3 ✓ Ro5 ✓ Clean C[C@](COC(=O)CCCC(=O)O)([C@H](C(=O)O)N\C=C\C=O)…
SM2 RCSB PDB P62593 319.1 Da LogP 0.86 TPSA 106.9 ✓ Ro5 ✓ Clean B([C@H](c1cccc(c1)C(=O)O)NC(=O)Cc2cccs2)(O)O
TAU RCSB PDB P0AD64 125.1 Da LogP -1.17 TPSA 80.4 ✓ Ro5 ✓ Clean C(CS(=O)(=O)O)N
TBE RCSB PDB P0AD64 302.3 Da LogP -1.60 TPSA 131.2 ✓ Ro5 ✓ Clean C[C@](Cn1ccnn1)([C@H](C(=O)O)N\C=C/C=O)S(=O)=O
TBI RCSB PDB P0AD64 302.3 Da LogP -1.60 TPSA 131.2 ✓ Ro5 ✓ Clean C[C@](Cn1ccnn1)([C@H](C(=O)O)N\C=C\C=O)S(=O)=O
TEM RCSB PDB P0AD64 157.2 Da LogP -0.76 TPSA 66.4 ✓ Ro5 ✓ Clean C(C=O)C(CN\C=C\C=O)O
TSL RCSB PDB P0AD64 235.3 Da LogP -0.26 TPSA 103.7 ✓ Ro5 ✓ Clean CC(C)([C@H](C(=O)O)N/C=C/C=O)[S@@](=O)O
WY2 RCSB PDB P0AD64 363.4 Da LogP 2.17 TPSA 104.3 ✓ Ro5 ✓ Clean c1c(nc2n1c3c(s2)CCC3)[C@H]4C(=CN=C(CS4)C(=O)O)C…
WY4 RCSB PDB P0AD64 307.3 Da LogP 0.81 TPSA 93.8 ✓ Ro5 ✓ Clean c1c(nc2n1CCOC2)[C@H]3C(=CN=C(CS3)C(=O)O)C=O
XE RCSB PDB P62593 131.3 Da LogP 0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Xe]
ZXM RCSB PDB P0AD64 324.1 Da LogP -1.22 TPSA 137.6 ✓ Ro5 ✓ Clean B([C@H](Cn1cc(nn1)C(=O)O)NC(=O)Cc2cccs2)(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.

Structure

Chemistry

ChEMBL CHEMBL4114803 ChEMBL CHEMBL212163 ChEMBL CHEMBL263746 ChEMBL CHEMBL4111477 ChEMBL CHEMBL122450 ChEMBL CHEMBL124416 ChEMBL CHEMBL212760 ChEMBL CHEMBL378119 ChEMBL CHEMBL379856 ChEMBL CHEMBL380061 ChEMBL CHEMBL4114749 ChEMBL CHEMBL4106598 ChEMBL CHEMBL378041 ChEMBL CHEMBL385593 ChEMBL CHEMBL4106976 ChEMBL CHEMBL222375 ChEMBL CHEMBL35987 ChEMBL CHEMBL425963 ChEMBL CHEMBL4533632 ChEMBL CHEMBL4109897 ChEMBL CHEMBL212478 ChEMBL CHEMBL377382 ChEMBL CHEMBL4114669 ChEMBL CHEMBL268919 ChEMBL CHEMBL331090 ChEMBL CHEMBL379440 ChEMBL CHEMBL377001 ChEMBL CHEMBL388778 ChEMBL CHEMBL433726 ChEMBL CHEMBL6533 ChEMBL CHEMBL1689063 ChEMBL CHEMBL222922 ChEMBL CHEMBL416561 ChEMBL CHEMBL222866 ChEMBL CHEMBL4114818 ChEMBL CHEMBL211143 ChEMBL CHEMBL222758 ChEMBL CHEMBL396872 ChEMBL CHEMBL4114672 ChEMBL CHEMBL396998 ChEMBL CHEMBL355558 ChEMBL CHEMBL375172 ChEMBL CHEMBL397438 ChEMBL CHEMBL6469 ChEMBL CHEMBL169392 ChEMBL CHEMBL395017 ChEMBL CHEMBL230859 ChEMBL CHEMBL4114697 ChEMBL CHEMBL3989959 ChEMBL BZB ChEMBL CHEMBL4115687 ChEMBL CHEMBL235293 ChEMBL CHEMBL235526 ChEMBL J01 ChEMBL CHEMBL238243 ChEMBL CHEMBL397522 ChEMBL CHEMBL4114754 ChEMBL CHEMBL230332 ChEMBL CHEMBL1578600 ChEMBL CHEMBL1206880 ChEMBL CHEMBL235292 ChEMBL CHEMBL36657 ChEMBL VA1 ChEMBL CHEMBL396753 ChEMBL 2GK ChEMBL CHEMBL6461 ChEMBL CHEMBL395398 ChEMBL CHEMBL4114694 ChEMBL CHEMBL235308 ChEMBL CHEMBL33711 ChEMBL CHEMBL33950 ChEMBL CHEMBL396509 ChEMBL CHEMBL230226 ChEMBL CHEMBL8290 ChEMBL TAZ ChEMBL CHEMBL4114788 ChEMBL CHEMBL6678 ChEMBL CHEMBL4114663 ChEMBL CHEMBL167539 ChEMBL CHEMBL353422 ChEMBL CHEMBL4114696 ChEMBL CHEMBL269471 ChEMBL CHEMBL4114757 ChEMBL CHEMBL236203 ChEMBL CHEMBL395186 ChEMBL CHEMBL237390 ChEMBL CHEMBL353613 ChEMBL CHEMBL4114713 ChEMBL CHEMBL366664 ChEMBL CHEMBL4114769 ChEMBL CHEMBL1492629 ChEMBL CHEMBL287095 ChEMBL CHEMBL4114759 ChEMBL CHEMBL283629 ChEMBL CHEMBL284539 ChEMBL CHEMBL4114790 ChEMBL CHEMBL235951 ChEMBL CHEMBL355165 ChEMBL CHEMBL287670 ChEMBL CHEMBL1573007