Protein target profile

PA5514

beta-lactamase

Genome: NC_002516.2

Gene: PA5514 3D evidence: AlphaFold DB model UniProt G3XCV9

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Length 262

Pocket druggability 0.694

Ligand records 58

EC / GO 0 / 3

Target summary

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

4 signals

Strengths

Risks / watch

No major risk signal surfaced in the loaded evidence.

Missing evidence

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein.

How to read 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 TPW 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.

Overview

Basic information about this protein and its source genome.

Accession: PA5514
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA5514
Status: annotated
Amino acids: 262
3D evidence: AlphaFold DB model

GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0008658 Binding to penicillin, an antibiotic that contains the condensed beta-lactamthiazolidine ring system. GO:0071555 A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Gut microbiome off-target: Hit
Essential (DEG): N
Localization: Unknown

Selected pocket evidence

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.694

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0008658 Binding to penicillin, an antibiotic that contains the condensed beta-lactamthiazolidine ring system.
GO:0071555 A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records

Show feature table

Start	End	DB	Term	Name
9	262	Gene3D	G3DSA:3.40.710.10	-
9	262	InterPro	IPR012338	Beta-lactamase/transpeptidase-like
4	12	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
1	18	SignalP_EUK	SignalP-noTM	SignalP-noTM
1	18	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
1	3	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
16	262	FunFam	G3DSA:3.40.710.10:FF:000019	Beta-lactamase
55	250	Pfam	PF00905	Penicillin binding protein transpeptidase domain
55	250	InterPro	IPR001460	Penicillin-binding protein, transpeptidase
34	251	SUPERFAMILY	SSF56601	beta-lactamase/transpeptidase-like
34	251	InterPro	IPR012338	Beta-lactamase/transpeptidase-like
1	18	Phobius	SIGNAL_PEPTIDE	Signal peptide region
13	18	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
19	262	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.

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.

Loading 3D structure...

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Structural evidence

0 + 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
AlphaFold DB PA5514	AlphaFold DB	—	—	full sequence	—	Viewing

Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

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

Site 1 FPocket #1

0.694

Show in viewer

Site 2 FPocket #3

0.63

Show in viewer

Site 3 FPocket #5

0.272

Show in viewer

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.

58 records

Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 58 via homologs

Structural ligands 7 0 loaded crystals

Bioactive compounds 2 49 ZINC proposed compounds

Drug-like & clean 53 0 PAINS alerts

Best available ligand signal

4J6 PDB via homolog 422.5 Da · LogP -1.66 · TPSA 170.8 Open detail RCSB PDB

Detail RCSB PDB 4J6 PDB via homolog

Detail RCSB PDB CEF PDB via homolog

Detail RCSB PDB CTJ PDB via homolog

Detail RCSB PDB FLC PDB via homolog

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
4J6 RCSB PDB	5WI7	I6YCI1	422.5 Da LogP -1.66 TPSA 170.8	1 viol.	✓ Clean	`C[C@@H]1[C@@H](NC(=C1S[C@H]2C[C@H](NC2)CNS(=O)(…`
CEF RCSB PDB	5WI3	I6YCI1	397.4 Da LogP -0.09 TPSA 156.3	✓ Ro5	✓ Clean	`CO/N=C(/c1csc(n1)N)\C(=O)NC(C=O)C2N=C(C(=C)CS2)…`
CTJ RCSB PDB	4X55	G5DE28	549.6 Da LogP -0.02 TPSA 197.2	2 viol.	✓ Clean	`CC(C)(C(=O)O)O/N=C(/c1csc(n1)N)\C(=O)N[C@H](C=O…`
FLC RCSB PDB	4JF5	Q9L4P2	189.1 Da LogP -5.25 TPSA 140.6	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O`
ID1 RCSB PDB	5WIB	I6YCI1	301.4 Da LogP -0.43 TPSA 125.3	✓ Ro5	✓ Clean	`C[C@H]([C@@H](C=O)[C@H]1C[C@H](C(=N1)C(=O)O)SCC…`
KE1 RCSB PDB	6N6V	Q9L4P2	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…`
MER RCSB PDB	4JF4	Q9L4P2	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…`

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
RM9 ChEMBL	Q9L4P2	9.13	222.0 Da LogP 1.25 TPSA 66.8	✓ Ro5	✓ Clean	`B1([C@@H]2C[C@@H]2c3ccc(c(c3O1)C(=O)O)F)O`
TAZ ChEMBL	Q50H31	6.80	300.3 Da LogP -1.52 TPSA 122.5	✓ Ro5	✓ Clean	`C[C@@]1([C@@H](N2[C@H](S1(=O)=O)CC2=O)C(=O)O)Cn…`

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
ZINC1483277 ZINC	1.000	300.3 Da LogP -1.52 TPSA 122.5	✓ Ro5	✓ Clean	`C[C@]1(Cn2ccnn2)[C@@H](C(=O)O)N2C(=O)C[C@H]2S1(…`
ZINC3781867 ZINC	1.000	300.3 Da LogP -1.52 TPSA 122.5	✓ Ro5	✓ Clean	`C[C@@]1(Cn2ccnn2)[C@H](C(=O)O)N2C(=O)C[C@H]2S1(…`
ZINC3787060 ZINC	1.000	300.3 Da LogP -1.52 TPSA 122.5	✓ Ro5	✓ Clean	`C[C@]1(Cn2ccnn2)[C@H](C(=O)O)N2C(=O)C[C@H]2S1(=…`
ZINC3831502 ZINC	1.000	300.3 Da LogP -1.52 TPSA 122.5	✓ Ro5	✓ Clean	`C[C@]1(Cn2ccnn2)[C@H](C(=O)O)N2C(=O)C[C@@H]2S1(…`
ZINC3831504 ZINC	1.000	300.3 Da LogP -1.52 TPSA 122.5	✓ Ro5	✓ Clean	`C[C@]1(Cn2ccnn2)[C@@H](C(=O)O)N2C(=O)C[C@@H]2S1…`
ZINC897245 ZINC	1.000	300.3 Da LogP -1.52 TPSA 122.5	✓ Ro5	✓ Clean	`C[C@@]1(Cn2ccnn2)[C@@H](C(=O)O)N2C(=O)C[C@@H]2S…`
ZINC34256277 ZINC	0.780	317.4 Da LogP -0.55 TPSA 145.6	✓ Ro5	✓ Clean	`C[C@H](O)[C@H](C(=O)O)[C@@H]1C[C@H](SCC/N=C/N)C…`
ZINC1532902 ZINC	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC2018106 ZINC	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
ZINC36411089 ZINC	0.700	466.5 Da LogP 1.72 TPSA 111.5	✓ Ro5	✓ Clean	`C[C@]1(Cn2ccnn2)[C@H](C(=O)OC(c2ccccc2)c2ccccc2…`
ZINC141067446 ZINC	0.685	315.3 Da LogP -2.09 TPSA 113.5	✓ Ro5	✓ Clean	`C[n+]1ccn(C[C@@]2(C)[C@H](C(=O)O)N3C(=O)C[C@H]3…`
ZINC3593496 ZINC	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC3593497 ZINC	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC14686440 ZINC	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…`
ZINC14686442 ZINC	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=O…`
ZINC14686444 ZINC	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=…`
ZINC1857792272 ZINC	0.615	324.1 Da LogP 0.86 TPSA 91.3	✓ Ro5	✓ Clean	`COCC(=O)OCOC(=O)c1c(F)ccc2c1OB(O)[C@@H]1C[C@H]21`
ZINC1857792242 ZINC	0.604	352.1 Da LogP 0.78 TPSA 108.4	✓ Ro5	✓ Clean	`CC(=O)OCC(=O)OCOC(=O)c1c(F)ccc2c1OB(O)[C@@H]1C[…`
ZINC13398039 ZINC	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC2528012 ZINC	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC48047558 ZINC	0.567	428.5 Da LogP 1.27 TPSA 106.5	✓ Ro5	✓ Clean	`C[C@@]1(Cn2ccc(-n3cccc3)c2-n2cccc2)[C@H](C(=O)O…`
ZINC146315135 ZINC	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@@](O)(CC(=O)O)C(=O)O`
ZINC146315336 ZINC	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@](O)(CC(=O)O)C(=O)O`
ZINC390823133 ZINC	0.551	390.5 Da LogP -0.96 TPSA 141.8	✓ Ro5	✓ Clean	`C[C@@H]1C(=O)N2C(C(=O)O)=C(S[C@@H]3CN[C@H](CNS(…`
ZINC390823134 ZINC	0.551	390.5 Da LogP -0.96 TPSA 141.8	✓ Ro5	✓ Clean	`C[C@@H]1C(=O)N2C(C(=O)O)=C(S[C@@H]3CN[C@H](CNS(…`
ZINC390823135 ZINC	0.551	390.5 Da LogP -0.96 TPSA 141.8	✓ Ro5	✓ Clean	`C[C@@H]1C(=O)N2C(C(=O)O)=C(S[C@@H]3CN[C@H](CNS(…`
ZINC390823136 ZINC	0.551	390.5 Da LogP -0.96 TPSA 141.8	✓ Ro5	✓ Clean	`C[C@@H]1C(=O)N2C(C(=O)O)=C(S[C@@H]3CN[C@H](CNS(…`
ZINC2086 ZINC	0.542	233.2 Da LogP -0.79 TPSA 91.8	✓ Ro5	✓ Clean	`CC1(C)[C@@H](C(=O)O)N2C(=O)C[C@H]2S1(=O)=O`
ZINC2548423 ZINC	0.542	233.2 Da LogP -0.79 TPSA 91.8	✓ Ro5	✓ Clean	`CC1(C)[C@H](C(=O)O)N2C(=O)C[C@@H]2S1(=O)=O`
ZINC336994 ZINC	0.542	233.2 Da LogP -0.79 TPSA 91.8	✓ Ro5	✓ Clean	`CC1(C)[C@@H](C(=O)O)N2C(=O)C[C@@H]2S1(=O)=O`
ZINC897244 ZINC	0.542	233.2 Da LogP -0.79 TPSA 91.8	✓ Ro5	✓ Clean	`CC1(C)[C@H](C(=O)O)N2C(=O)C[C@H]2S1(=O)=O`
ZINC21984184 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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)…`
ZINC13398014 ZINC	0.522	220.2 Da LogP -1.07 TPSA 110.1	✓ Ro5	✓ Clean	`COC(=O)CC(O)(CC(=O)OC)C(=O)O`
ZINC3861629 ZINC	0.522	206.1 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C(O)(CC(=O)O)CC(=O)O`
ZINC100969993 ZINC	0.500	359.5 Da LogP 2.70 TPSA 123.9	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC100969996 ZINC	0.500	359.5 Da LogP 2.70 TPSA 123.9	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC1711854 ZINC	0.500	248.2 Da LogP -0.13 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)CC(CC(=O)O)(CC(=O)O)CC(=O)O`
ZINC2049389096 ZINC	0.500	317.4 Da LogP -0.34 TPSA 143.1	✓ Ro5	✓ Clean	`C[C@H](O)[C@H](C(=O)O)[C@H]1C[C@@H](SCCNC=N)C(C…`
ZINC2049389097 ZINC	0.500	317.4 Da LogP -0.34 TPSA 143.1	✓ Ro5	✓ Clean	`C[C@H](O)[C@H](C(=O)O)[C@H]1C[C@H](SCCNC=N)C(C(…`
ZINC2049389098 ZINC	0.500	317.4 Da LogP -0.34 TPSA 143.1	✓ Ro5	✓ Clean	`C[C@H](O)[C@H](C(=O)O)[C@@H]1C[C@@H](SCCNC=N)C(…`

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.