Protein target profile

KP13_04408

Elongation factor P-like protein

Genome: KpKP13 Gene: AHE43556.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GVI2

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Length 190

Pocket druggability 0.021

Direct ligand evidence 0 51 total records

Functional annotation 0 EC 5 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.

Main supporting evidence

Risks to review

Microbiome similarity 120 of 4744 screened genomes (2.5%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.02.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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: 2.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 52.91 Higher values support similarity to known essential genes.
DEG E-value: 1.15e-72 Smaller values mean stronger essential-gene similarity.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 93.53 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

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 0.021

Structure A0A0H3GVI2

Pocket Pocket 3

P2Rank

Structure A0A0H3GVI2

Pocket No pockets

ColabFold model

FPocket 0.093 · Pocket 4

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 120 / 4744 genomes with a hit

Prevalence 2.5%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A0A0H3GVI2

Sequence

Primary amino-acid sequence viewer.

MPRANEIKKGMVLNYNGKLLIVKNIDIQSPSARGAATLYKMRFSDVRTGLKVEERFKGDDIVDTVTLTRRFVDFSYVDGNEYVFMDKEDYTPYTFTKEQIEEELQFIPEGGMPDMQVLTWDGQLLALELPQTVDLEIIETAPGIKGASASSRTKPATMSTGLVIQVPEYLTTGEKIRIHIEECRYMGRAD

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0003746 Functions in chain elongation during polypeptide synthesis at the ribosome.
GO:0043043 The chemical reactions and pathways resulting in the formation of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. This may include the translation of a precursor protein and its subsequent processing into a functional peptide.
GO:0006414 The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

37 records

Show feature table

Start	End	DB	Term	Name
1	65	SUPERFAMILY	SSF50104	Translation proteins SH3-like domain
1	65	InterPro	IPR008991	Translation protein SH3-like domain superfamily
66	130	Gene3D	G3DSA:2.40.50.140	-
66	130	InterPro	IPR012340	Nucleic acid-binding, OB-fold
3	189	PANTHER	PTHR30053	ELONGATION FACTOR P
3	189	InterPro	IPR020599	Translation elongation factor P/YeiP
1	190	PIRSF	PIRSF005901	EF-P
1	190	InterPro	IPR020599	Translation elongation factor P/YeiP
68	130	CDD	cd04470	S1_EF-P_repeat_1
68	130	InterPro	IPR001059	Translation elongation factor P/YeiP, central
69	125	SMART	SM01185	EFP_2
69	125	InterPro	IPR001059	Translation elongation factor P/YeiP, central
132	190	Gene3D	G3DSA:2.40.50.140	-
132	190	InterPro	IPR012340	Nucleic acid-binding, OB-fold
66	130	FunFam	G3DSA:2.40.50.140:FF:000053	Elongation factor P-like protein
72	124	Pfam	PF01132	Elongation factor P (EF-P) OB domain
72	124	InterPro	IPR001059	Translation elongation factor P/YeiP, central
4	62	Pfam	PF08207	Elongation factor P (EF-P) KOW-like domain
4	62	InterPro	IPR013185	Translation elongation factor, KOW-like
3	189	NCBIfam	TIGR02178	elongation factor P-like protein YeiP
3	189	InterPro	IPR011897	Translation elongation factor P-like, YeiP
132	189	SUPERFAMILY	SSF50249	Nucleic acid-binding proteins
132	189	InterPro	IPR012340	Nucleic acid-binding, OB-fold
133	188	CDD	cd05794	S1_EF-P_repeat_2
133	188	InterPro	IPR015365	Elongation factor P, C-terminal
132	190	FunFam	G3DSA:2.40.50.140:FF:000004	Elongation factor P
133	188	SMART	SM00841	Elong_fact_P_C_2
2	189	Hamap	MF_00646	Elongation factor P-like protein [yeiP].
2	189	InterPro	IPR011897	Translation elongation factor P-like, YeiP
154	173	ProSitePatterns	PS01275	Elongation factor P signature.
154	173	InterPro	IPR013852	Translation elongation factor P/YeiP, conserved site
68	130	SUPERFAMILY	SSF50249	Nucleic acid-binding proteins
68	130	InterPro	IPR012340	Nucleic acid-binding, OB-fold
1	64	Gene3D	G3DSA:2.30.30.30	-
1	64	InterPro	IPR014722	Ribosomal protein L2, domain 2
1	64	FunFam	G3DSA:2.30.30.30:FF:000011	Elongation factor P-like protein
133	188	Pfam	PF09285	Elongation factor P, C-terminal

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.

Download VMD script Full viewer

No pockets are loaded yet for the displayed AlphaFold DB model AF_A0A0H3GVI2 structure. Run experimental pocket backfill to show FPocket/P2Rank overlays on this structure.

Loading 3D structure...

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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'.

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_A0A0H3GVI2	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_04408	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.

51 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 1 records from similar proteins

Structural ligands 1 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

KAA PDB via homolog 474.5 Da · LogP -3.14 · TPSA 243.8 Open detail RCSB PDB

ZINC168710640 ZINC proposed compound · Tanimoto 0.809 Detail ZINC

ZINC168710738 ZINC proposed compound · Tanimoto 0.809 Detail ZINC

ZINC1083817667 ZINC proposed compound · Tanimoto 0.768 Detail ZINC

ZINC936069053 ZINC proposed compound · Tanimoto 0.768 Detail ZINC

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, 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
KAA RCSB PDB	3A5Z	P0A6N4	474.5 Da LogP -3.14 TPSA 243.8	2 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`

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).

No ChEMBL hits found through similar proteins.

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
ZINC168710640 ZINC	0.809	474.5 Da LogP -4.00 TPSA 260.9	2 viol.	✓ Clean	`NC(=O)CC[C@H](N)C(=O)NS(=O)(=O)OC[C@H]1O[C@@H](…`
ZINC168710738 ZINC	0.809	474.5 Da LogP -4.00 TPSA 260.9	2 viol.	✓ Clean	`NC(=O)CC[C@H](N)C(=O)NS(=O)(=O)OC[C@H]1O[C@@H](…`
ZINC1083817667 ZINC	0.768	459.5 Da LogP -2.22 TPSA 217.8	1 viol.	✓ Clean	`CC(C)C[C@@H](N)C(=O)NS(=O)(=O)OC[C@H]1O[C@@H](n…`
ZINC936069053 ZINC	0.768	459.5 Da LogP -2.22 TPSA 217.8	1 viol.	✓ Clean	`CC(C)C[C@@H](N)C(=O)NS(=O)(=O)OC[C@@H]1O[C@H](n…`
ZINC14967098 ZINC	0.731	403.4 Da LogP -3.64 TPSA 217.8	1 viol.	✓ Clean	`NCC(=O)NS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc…`
ZINC218033334 ZINC	0.731	403.4 Da LogP -3.64 TPSA 217.8	1 viol.	✓ Clean	`NCC(=O)NS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc…`
ZINC218033425 ZINC	0.731	403.4 Da LogP -3.64 TPSA 217.8	1 viol.	✓ Clean	`NCC(=O)NS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc…`
ZINC218033503 ZINC	0.731	403.4 Da LogP -3.64 TPSA 217.8	1 viol.	✓ Clean	`NCC(=O)NS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc…`
ZINC936069043 ZINC	0.718	459.5 Da LogP -2.22 TPSA 217.8	1 viol.	✓ Clean	`CC[C@@H](C)[C@@H](N)C(=O)NS(=O)(=O)OC[C@@H]1O[C…`
ZINC4824650 ZINC	0.653	394.4 Da LogP -2.40 TPSA 200.5	2 viol.	✓ Clean	`NCCCC[C@@H](N)C(=O)N[C@@H]1[C@H](CO)O[C@H](n2cn…`
ZINC4824652 ZINC	0.653	394.4 Da LogP -2.40 TPSA 200.5	2 viol.	✓ Clean	`NCCCC[C@@H](N)C(=O)N[C@@H]1[C@H](CO)O[C@@H](n2c…`
ZINC4824654 ZINC	0.653	394.4 Da LogP -2.40 TPSA 200.4	2 viol.	✓ Clean	`NCCCC[C@@H](N)C(=O)N[C@H]1[C@H](O)[C@@H](n2cnc3…`
ZINC4824655 ZINC	0.653	394.4 Da LogP -2.40 TPSA 200.4	2 viol.	✓ Clean	`NCCCC[C@@H](N)C(=O)N[C@H]1[C@H](O)[C@H](n2cnc3c…`
ZINC12405780 ZINC	0.646	346.3 Da LogP -2.75 TPSA 188.7	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COS(N)(=O)=O)[C@@H]…`
ZINC12502832 ZINC	0.646	346.3 Da LogP -2.75 TPSA 188.7	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COS(N)(=O)=O)[C@@H]…`
ZINC79460727 ZINC	0.646	346.3 Da LogP -2.75 TPSA 188.7	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COS(N)(=O)=O)[C@H](…`
ZINC79460732 ZINC	0.646	346.3 Da LogP -2.75 TPSA 188.7	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COS(N)(=O)=O)[C@H](…`
ZINC14967079 ZINC	0.600	461.4 Da LogP -2.95 TPSA 258.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COS(=O)(=O)/N=C(\O)…`
ZINC31260554 ZINC	0.597	474.5 Da LogP -3.16 TPSA 264.4	2 viol.	✓ Clean	`NC(=O)CC[C@H](N)/C(O)=N/S(=O)(=O)OC[C@H]1O[C@@H…`
ZINC31976683 ZINC	0.597	474.5 Da LogP -3.16 TPSA 264.4	2 viol.	✓ Clean	`NC(=O)CC[C@H](N)/C(O)=N/S(=O)(=O)OC[C@H]1O[C@@H…`
ZINC13547650 ZINC	0.597	309.3 Da LogP -1.41 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)…`
ZINC4823971 ZINC	0.597	309.3 Da LogP -1.41 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O…`
ZINC4823975 ZINC	0.597	309.3 Da LogP -1.41 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)OC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](…`
ZINC4823980 ZINC	0.597	309.3 Da LogP -1.41 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O…`
ZINC4823984 ZINC	0.597	309.3 Da LogP -1.41 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)OC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](…`
ZINC24951137 ZINC	0.581	417.4 Da LogP -2.41 TPSA 221.3	1 viol.	✓ Clean	`C[C@H](N)/C(O)=N/S(=O)(=O)OC[C@H]1O[C@@H](n2cnc…`
ZINC33821383 ZINC	0.571	459.5 Da LogP -1.38 TPSA 221.3	1 viol.	✓ Clean	`CC(C)C[C@H](N)/C(O)=N/S(=O)(=O)OC[C@H]1O[C@@H](…`
ZINC49014951 ZINC	0.569	416.4 Da LogP -2.76 TPSA 216.8	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CS(=O)(=O)CC[C@H](N)…`
ZINC49014955 ZINC	0.569	416.4 Da LogP -2.76 TPSA 216.8	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CS(=O)(=O)CC[C@@H](N…`
ZINC1574270 ZINC	0.568	421.4 Da LogP -0.26 TPSA 162.7	1 viol.	✓ Clean	`Cc1ccc(S(=O)(=O)OC[C@@H]2O[C@H](n3cnc4c(N)ncnc4…`
ZINC3861767 ZINC	0.568	421.4 Da LogP -0.26 TPSA 162.7	1 viol.	✓ Clean	`Cc1ccc(S(=O)(=O)OC[C@H]2O[C@@H](n3cnc4c(N)ncnc4…`
ZINC5487110 ZINC	0.568	425.6 Da LogP -0.00 TPSA 171.3	1 viol.	✓ Clean	`NCCCCC[C@@H](CCN)SC[C@@H]1O[C@H](n2cnc3c(N)ncnc…`
ZINC5487111 ZINC	0.568	425.6 Da LogP -0.00 TPSA 171.3	1 viol.	✓ Clean	`NCCCCC[C@@H](CCN)SC[C@@H]1O[C@@H](n2cnc3c(N)ncn…`
ZINC5487114 ZINC	0.568	425.6 Da LogP -0.00 TPSA 171.3	1 viol.	✓ Clean	`NCCCCC[C@@H](CCN)SC[C@@H]1O[C@H](n2cnc3c(N)ncnc…`
ZINC5487117 ZINC	0.568	425.6 Da LogP -0.00 TPSA 171.3	1 viol.	✓ Clean	`NCCCCC[C@@H](CCN)SC[C@@H]1O[C@@H](n2cnc3c(N)ncn…`
ZINC13518964 ZINC	0.565	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515 ZINC	0.565	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC1571045 ZINC	0.565	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC1842158 ZINC	0.565	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC2046931 ZINC	0.565	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310 ZINC	0.565	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891 ZINC	0.565	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893 ZINC	0.565	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180 ZINC	0.565	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156 ZINC	0.565	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897 ZINC	0.565	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O…`
ZINC4806442 ZINC	0.565	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC8613167 ZINC	0.565	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC13488353 ZINC	0.558	459.5 Da LogP -1.38 TPSA 221.3	1 viol.	✓ Clean	`CC[C@H](C)[C@H](N)/C(O)=N/S(=O)(=O)OC[C@H]1O[C@…`
ZINC13522400 ZINC	0.556	400.4 Da LogP -2.42 TPSA 199.7	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[S@](=O)CC[C@H](N)…`

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.