Protein profile

KP13_01389

Beta-lactamase OXA-9

Genome: KpKP13

Gene: bla AHE47441.1 Structure source: AlphaFold + ColabFold UniProt B2CBF6

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Amino acids 279

Annotations 5

Features 16

PDB binders 6

Druggability 0.475

Overview

Basic information about this protein and its source genome.

Accession: KP13_01389
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: bla AHE47441.1
Status: annotated
Amino acids: 279
Structure source: AlphaFold + ColabFold

3.5.2.6

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:0008658 Binding to penicillin, an antibiotic that contains the condensed beta-lactamthiazolidine ring system. 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.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Unknown
ColabFold pLDDT: 91.36

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.475

Structure B2CBF6

Pocket Pocket 1

P2Rank 0.464

Structure B2CBF6

Pocket Pocket 1

ColabFold model

FPocket 0.773 · Pocket 4

P2Rank 0.227 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 3 / 4744 genomes with a hit

Normalized 0.001

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

3.5.2.6

Gene Ontology (GO)

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:0008658 Binding to penicillin, an antibiotic that contains the condensed beta-lactamthiazolidine ring system.
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.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records

Show feature table

Start	End	DB	Term	Name
26	279	Gene3D	G3DSA:3.40.710.10	-
26	279	InterPro	IPR012338	Beta-lactamase/transpeptidase-like
1	28	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
1	28	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
30	279	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
22	29	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
10	21	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
38	265	SUPERFAMILY	SSF56601	beta-lactamase/transpeptidase-like
38	265	InterPro	IPR012338	Beta-lactamase/transpeptidase-like
61	71	ProSitePatterns	PS00337	Beta-lactamase class-D active site.
61	71	InterPro	IPR002137	Beta-lactamase, class-D active site
1	20	SignalP_EUK	SignalP-noTM	SignalP-noTM
1	29	Phobius	SIGNAL_PEPTIDE	Signal peptide region
48	249	Pfam	PF00905	Penicillin binding protein transpeptidase domain
48	249	InterPro	IPR001460	Penicillin-binding protein, transpeptidase
1	9	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

Loading 3D structure...

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_B2CBF6	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_01389	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
1				0.475
4				0.259

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				6.04	0.298
2				0.84	0.003

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
4				0.773

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Score	Probability
1	2.19	0.053
2	1.15	0.009
3	1.03	0.006

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

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, 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
1S6	2IWD	P0A0B0	403.5 Da LogP 1.84 TPSA 121.5	✓ Ro5	✓ Clean	`Cc1c(c(no1)c2ccccc2)C(=O)N[C@H](C=O)[C@@H]3N[C@…`
5R7	5CTN	A8FFI9	422.5 Da LogP -1.65 TPSA 171.2	✓ Ro5	✓ Clean	`C[C@H]1[C@H](C(=N[C@H]1[C@H](C=O)[C@@H](C)O)C(=…`
DRW	3ISG	P13661	422.5 Da LogP -1.65 TPSA 171.2	✓ Ro5	✓ Clean	`C[C@H]1[C@@H](C(=N[C@H]1[C@H](C=O)[C@@H](C)O)C(…`
FLC	5CTM	A8FFI9	189.1 Da LogP -5.25 TPSA 140.6	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O`
MER	1H8Y	Q51400	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…`
NXL	6O9S	P0A0B1	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`

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
CHEMBL6461	P13661	7.00	292.2 Da LogP -5.07 TPSA 118.4	✓ Ro5	✓ Clean	`C[C@]1(/C=C/C#N)[C@H](C(=O)[O-])N2C(=O)C[C@H]2S…`
CHEMBL1689063	P13661	6.89	265.2 Da LogP -1.53 TPSA 130.2	✓ Ro5	✓ Clean	`NC(=O)[C@@H]1CC[C@@H]2CN1C(=O)N2OS(=O)(=O)O`

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
ZINC1551650	1.000	265.2 Da LogP -1.53 TPSA 130.2	✓ Ro5	✓ Clean	`NC(=O)[C@H]1CC[C@H]2CN1C(=O)N2OS(=O)(=O)O`
ZINC33979726	1.000	265.2 Da LogP -1.53 TPSA 130.2	✓ Ro5	✓ Clean	`NC(=O)[C@H]1CC[C@@H]2CN1C(=O)N2OS(=O)(=O)O`
ZINC3966153	1.000	265.2 Da LogP -1.53 TPSA 130.2	✓ Ro5	✓ Clean	`NC(=O)[C@@H]1CC[C@H]2CN1C(=O)N2OS(=O)(=O)O`
ZINC9302239	1.000	265.2 Da LogP -1.53 TPSA 130.2	✓ Ro5	✓ Clean	`NC(=O)[C@@H]1CC[C@@H]2CN1C(=O)N2OS(=O)(=O)O`
ZINC15415787	0.767	419.5 Da LogP 1.73 TPSA 141.8	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2)c1C(=O)N[C@H](C(=O)O)[C@@H]1N[…`
ZINC15415790	0.767	419.5 Da LogP 1.73 TPSA 141.8	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2)c1C(=O)N[C@@H](C(=O)O)[C@@H]1N…`
ZINC15415793	0.767	419.5 Da LogP 1.73 TPSA 141.8	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2)c1C(=O)N[C@H](C(=O)O)[C@H]1N[C…`
ZINC15415796	0.767	419.5 Da LogP 1.73 TPSA 141.8	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2)c1C(=O)N[C@@H](C(=O)O)[C@H]1N[…`
ZINC205497470	0.644	322.3 Da LogP -1.84 TPSA 145.3	✓ Ro5	✓ Clean	`CC(=O)NNC(=O)[C@@H]1CC[C@@H]2CN1C(=O)N2OS(=O)(=…`
ZINC207610051	0.638	324.3 Da LogP -2.00 TPSA 151.5	✓ Ro5	✓ Clean	`NCCONC(=O)[C@@H]1CC[C@@H]2CN1C(=O)N2OS(=O)(=O)O`
ZINC43206319	0.604	348.4 Da LogP -1.14 TPSA 128.3	✓ Ro5	✓ Clean	`O=C(NC1CCNCC1)[C@@H]1CC[C@@H]2CN1C(=O)N2OS(=O)(…`
ZINC79016947	0.604	348.4 Da LogP -1.14 TPSA 128.3	✓ Ro5	✓ Clean	`O=C(NC1CCNCC1)[C@H]1CC[C@H]2CN1C(=O)N2OS(=O)(=O…`
ZINC79016957	0.604	348.4 Da LogP -1.14 TPSA 128.3	✓ Ro5	✓ Clean	`O=C(NC1CCNCC1)[C@@H]1CC[C@H]2CN1C(=O)N2OS(=O)(=…`
ZINC204964427	0.595	247.2 Da LogP -0.49 TPSA 110.9	✓ Ro5	✓ Clean	`N#C[C@@H]1CC[C@@H]2CN1C(=O)N2OS(=O)(=O)O`
ZINC219376998	0.595	247.2 Da LogP -0.49 TPSA 110.9	✓ Ro5	✓ Clean	`N#C[C@H]1CC[C@H]2CN1C(=O)N2OS(=O)(=O)O`
ZINC219377080	0.595	247.2 Da LogP -0.49 TPSA 110.9	✓ Ro5	✓ Clean	`N#C[C@@H]1CC[C@H]2CN1C(=O)N2OS(=O)(=O)O`
ZINC1857655139	0.585	393.4 Da LogP -0.48 TPSA 145.5	✓ Ro5	✓ Clean	`CCOC(=O)C(C)(C)COS(=O)(=O)ON1C(=O)N2C[C@H]1CC[C…`
ZINC255993610	0.577	471.9 Da LogP 2.52 TPSA 141.8	✓ Ro5	✓ Clean	`Cc1onc(-c2c(F)cccc2Cl)c1C(=O)N[C@H](C(=O)O)[C@@…`
ZINC77292630	0.577	471.9 Da LogP 2.52 TPSA 141.8	✓ Ro5	✓ Clean	`Cc1onc(-c2c(F)cccc2Cl)c1C(=O)N[C@@H](C(=O)O)[C@…`
ZINC217927881	0.569	377.4 Da LogP -2.25 TPSA 157.4	✓ Ro5	✓ Clean	`O=C(NNC(=O)[C@@H]1CC[C@@H]2CN1C(=O)N2OS(=O)(=O)…`
ZINC114990116	0.563	275.3 Da LogP 0.87 TPSA 75.9	✓ Ro5	✓ Clean	`NC(=O)[C@@H]1CC[C@@H]2CN1C(=O)N2OCc1ccccc1`
ZINC114990119	0.563	275.3 Da LogP 0.87 TPSA 75.9	✓ Ro5	✓ Clean	`NC(=O)[C@@H]1CC[C@H]2CN1C(=O)N2OCc1ccccc1`
ZINC114990120	0.563	275.3 Da LogP 0.87 TPSA 75.9	✓ Ro5	✓ Clean	`NC(=O)[C@H]1CC[C@H]2CN1C(=O)N2OCc1ccccc1`
ZINC350748	0.534	244.3 Da LogP 2.79 TPSA 55.1	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2)c1C(=O)NC(C)C`
ZINC339747	0.533	272.3 Da LogP 3.57 TPSA 55.1	✓ Ro5	✓ Clean	`CCC(CC)NC(=O)c1c(-c2ccccc2)noc1C`
ZINC21984184	0.530	383.5 Da LogP -0.31 TPSA 110.2	✓ Ro5	✓ Clean	`C[C@@H]1C(S[C@@H]2CN[C@H](C(=O)N(C)C)C2)=C(C(=O…`
ZINC245204572	0.530	383.5 Da LogP -0.31 TPSA 110.2	✓ Ro5	✓ Clean	`C[C@@H]1C(S[C@@H]2CN[C@H](C(=O)N(C)C)C2)=C(C(=O…`
ZINC245204573	0.530	383.5 Da LogP -0.31 TPSA 110.2	✓ Ro5	✓ Clean	`C[C@H](O)[C@@H]1C(=O)N2C(C(=O)O)=C(S[C@@H]3CN[C…`
ZINC28636621	0.530	383.5 Da LogP -0.31 TPSA 110.2	✓ Ro5	✓ Clean	`C[C@@H](O)[C@H]1C(=O)N2C(C(=O)O)=C(S[C@@H]3CN[C…`
ZINC3808779	0.530	383.5 Da LogP -0.31 TPSA 110.2	✓ Ro5	✓ Clean	`C[C@@H](O)[C@H]1C(=O)N2C(C(=O)O)=C(S[C@@H]3CN[C…`
ZINC44672480	0.530	383.5 Da LogP -0.31 TPSA 110.2	✓ Ro5	✓ Clean	`C[C@@H](O)[C@H]1C(=O)N2C(C(=O)O)=C(S[C@@H]3CN[C…`
ZINC44675971	0.530	383.5 Da LogP -0.31 TPSA 110.2	✓ Ro5	✓ Clean	`C[C@@H](O)[C@@H]1C(=O)N2C(C(=O)O)=C(S[C@@H]3CN[…`
ZINC5736072	0.530	383.5 Da LogP -0.31 TPSA 110.2	✓ Ro5	✓ Clean	`C[C@H](O)[C@@H]1C(=O)N2C(C(=O)O)=C(S[C@@H]3CN[C…`
ZINC5736130	0.530	383.5 Da LogP -0.31 TPSA 110.2	✓ Ro5	✓ Clean	`C[C@H](O)[C@@H]1C(=O)N2C(C(=O)O)=C(S[C@@H]3CN[C…`
ZINC95486475	0.530	383.5 Da LogP -0.31 TPSA 110.2	✓ Ro5	✓ Clean	`C[C@H]1C(S[C@@H]2CN[C@H](C(=O)N(C)C)C2)=C(C(=O)…`
ZINC5443820	0.515	364.5 Da LogP 4.98 TPSA 55.1	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2)c1C(=O)N[C@@H](C)C12CC3CC(CC(C…`
ZINC5443822	0.515	364.5 Da LogP 4.98 TPSA 55.1	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2)c1C(=O)N[C@H](C)C12CC3CC(CC(C3…`
ZINC176196	0.508	306.4 Da LogP 4.14 TPSA 55.1	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2)c1C(=O)N[C@@H](C)c1ccccc1`
ZINC176198	0.508	306.4 Da LogP 4.14 TPSA 55.1	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2)c1C(=O)N[C@H](C)c1ccccc1`
ZINC13744465	0.500	286.4 Da LogP 3.81 TPSA 55.1	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2)c1C(=O)N[C@H](C)C(C)(C)C`
ZINC13744467	0.500	286.4 Da LogP 3.81 TPSA 55.1	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2)c1C(=O)N[C@@H](C)C(C)(C)C`
ZINC220881117	0.500	277.3 Da LogP -1.36 TPSA 130.2	✓ Ro5	✓ Clean	`CC1=C[C@@H]2CN(C(=O)N2OS(=O)(=O)O)[C@@H]1C(N)=O`
ZINC318763	0.500	334.4 Da LogP 4.40 TPSA 55.1	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2)c1C(=O)N[C@@H](C)CCc1ccccc1`
ZINC318764	0.500	334.4 Da LogP 4.40 TPSA 55.1	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2)c1C(=O)N[C@H](C)CCc1ccccc1`
ZINC860138	0.500	258.3 Da LogP 3.18 TPSA 55.1	✓ Ro5	✓ Clean	`CC[C@@H](C)NC(=O)c1c(-c2ccccc2)noc1C`
ZINC860139	0.500	258.3 Da LogP 3.18 TPSA 55.1	✓ Ro5	✓ Clean	`CC[C@H](C)NC(=O)c1c(-c2ccccc2)noc1C`
ZINC95955756	0.500	288.3 Da LogP 2.24 TPSA 92.4	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2)c1C(=O)N[C@@H](C)CC(=O)O`
ZINC95955757	0.500	288.3 Da LogP 2.24 TPSA 92.4	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2)c1C(=O)N[C@H](C)CC(=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.