Protein profile

KP13_02348

Glycine cleavage system transcriptional activator

Genome: KpKP13

Gene: gcvA AHE42918.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GUK6

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Amino acids 305

Annotations 4

Features 23

PDB binders 8

Druggability 0.293

Overview

Basic information about this protein and its source genome.

Accession: KP13_02348
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: gcvA AHE42918.1
Status: annotated
Amino acids: 305
Structure source: AlphaFold + ColabFold

GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons. GO:0043565 Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. GO:0006351 The synthesis of an RNA transcript from a DNA template.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 51.0
DEG E-value: 4.86e-101
Localization: Cytoplasmic
ColabFold pLDDT: 90.33

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 0.293

Structure A0A0H3GUK6

Pocket Pocket 4

P2Rank 0.722

Structure A0A0H3GUK6

Pocket Pocket 1

ColabFold model

FPocket 0.148 · Pocket 2

P2Rank 0.662 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 139 / 4744 genomes with a hit

Normalized 0.029

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
GO:0043565 Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
GO:0006351 The synthesis of an RNA transcript from a DNA template.

Sequence Features

Domain/signature hits from InterPro and related databases.

23 records

Show feature table

Start	End	DB	Term	Name
95	288	CDD	cd08432	PBP2_GcdR_TrpI_HvrB_AmpR_like
8	295	PANTHER	PTHR30537	HTH-TYPE TRANSCRIPTIONAL REGULATOR
164	261	FunFam	G3DSA:3.40.190.10:FF:000017	Glycine cleavage system transcriptional activator
98	288	Gene3D	G3DSA:3.40.190.10	-
3	89	Gene3D	G3DSA:1.10.10.10	-
3	89	InterPro	IPR036388	Winged helix-like DNA-binding domain superfamily
5	89	FunFam	G3DSA:1.10.10.10:FF:000038	Glycine cleavage system transcriptional activator
6	63	ProSiteProfiles	PS50931	LysR-type HTH domain profile.
6	63	InterPro	IPR000847	Transcription regulator HTH, LysR
93	296	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II
164	261	Gene3D	G3DSA:3.40.190.10	-
44	55	PRINTS	PR00039	LysR bacterial regulatory protein HTH signature
44	55	InterPro	IPR000847	Transcription regulator HTH, LysR
34	44	PRINTS	PR00039	LysR bacterial regulatory protein HTH signature
34	44	InterPro	IPR000847	Transcription regulator HTH, LysR
23	34	PRINTS	PR00039	LysR bacterial regulatory protein HTH signature
23	34	InterPro	IPR000847	Transcription regulator HTH, LysR
91	292	Pfam	PF03466	LysR substrate binding domain
91	292	InterPro	IPR005119	LysR, substrate-binding
8	67	Pfam	PF00126	Bacterial regulatory helix-turn-helix protein, lysR family
8	67	InterPro	IPR000847	Transcription regulator HTH, LysR
3	87	SUPERFAMILY	SSF46785	Winged helix DNA-binding domain
3	87	InterPro	IPR036390	Winged helix DNA-binding domain superfamily

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_A0A0H3GUK6	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02348	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
4				0.293
3				0.203

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	10.13	0.545
2	3.47	0.126
3	1.54	0.023

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				8.96	0.48
2				2.62	0.076

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

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
1PS	6G1B	Q8NP91	201.2 Da LogP -0.09 TPSA 61.1	✓ Ro5	✓ Clean	`c1cc[n+](cc1)CCCS(=O)(=O)[O-]`
AKG	5Y2V	P73862	146.1 Da LogP -0.50 TPSA 91.7	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)C(=O)O`
BEZ	2F7A	O68014	122.1 Da LogP 1.38 TPSA 37.3	✓ Ro5	✓ Clean	`c1ccc(cc1)C(=O)O`
FLC	5ZZO	A0A0D1IHL7	189.1 Da LogP -5.25 TPSA 140.6	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O`
FOR	6G1D	Q8NP91	30.0 Da LogP -0.18 TPSA 17.1	✓ Ro5	✓ Clean	`C=O`
MLI	4IHS	O68014	102.0 Da LogP -3.12 TPSA 80.3	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(=O)[O-]`
PEO	6G1B	Q8NP91	34.0 Da LogP 0.02 TPSA 40.5	✓ Ro5	✓ Clean	`OO`
RUB	5Z49	Q9F1R2	310.1 Da LogP -2.50 TPSA 191.0	1 viol.	✓ Clean	`C([C@H]([C@H](C(=O)COP(=O)(O)O)O)O)OP(=O)(O)O`

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
ZINC3870277	1.000	310.1 Da LogP -2.50 TPSA 191.0	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC3269660	0.824	254.2 Da LogP 2.45 TPSA 71.4	✓ Ro5	Alert	`O=C(O)c1ccc(C(=O)C(=O)c2ccccc2)cc1`
ZINC12502210	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)[C@@H](O)COP(=O…`
ZINC12502212	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)[C@H](O)COP(=O)…`
ZINC12502214	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@@H](O)[C@@H](O)COP(=…`
ZINC12502216	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@@H](O)[C@H](O)COP(=O…`
ZINC4523251	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@@H](O)[C@@H](O)COP(…`
ZINC4523255	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@@H](O)[C@H](O)COP(=…`
ZINC4523257	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)[C@@H](O)COP(=…`
ZINC4523259	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)[C@H](O)COP(=O…`
ZINC2504355	0.778	226.2 Da LogP 2.62 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccccc2)cc1`
ZINC1529626	0.724	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC1532567	0.724	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC1532851	0.724	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC30320708	0.724	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC31259596	0.724	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)CO`
ZINC31259600	0.724	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@@H](O)CO`
ZINC3869804	0.724	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@@H](O)CO`
ZINC3869805	0.724	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)CO`
ZINC1672966	0.688	210.2 Da LogP 2.75 TPSA 34.1	✓ Ro5	Alert	`O=C(C(=O)c1ccccc1)c1ccccc1`
ZINC34057267	0.684	274.3 Da LogP 4.72 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(-c3ccccc3)cc2)cc1`
ZINC1560408815	0.656	339.1 Da LogP -1.87 TPSA 214.1	1 viol.	✓ Clean	`[O]/C(COP(=O)(O)O)=C(/O)[C@H](O)[C@H](O)COP(=O)…`
ZINC114185151	0.647	298.2 Da LogP 2.15 TPSA 108.7	✓ Ro5	Alert	`O=C(O)c1ccc(C(=O)C(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC1590838	0.647	342.4 Da LogP 3.82 TPSA 68.3	✓ Ro5	Alert	`O=C(C(=O)c1ccc(C(=O)C(=O)c2ccccc2)cc1)c1ccccc1`
ZINC16133932	0.647	474.5 Da LogP 4.88 TPSA 102.4	✓ Ro5	Alert	`O=C(C(=O)c1ccc(C(=O)C(=O)c2ccc(C(=O)C(=O)c3cccc…`
ZINC5830339	0.645	231.1 Da LogP -2.68 TPSA 156.5	1 viol.	✓ Clean	`O=C(NO)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4521819	0.643	202.3 Da LogP 0.25 TPSA 58.3	✓ Ro5	✓ Clean	`O=S(=O)(O)CCC[n+]1ccccc1`
ZINC18140538	0.625	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC1070912	0.611	286.3 Da LogP 4.15 TPSA 34.1	✓ Ro5	✓ Clean	`O=C(c1ccccc1)c1ccc(C(=O)c2ccccc2)cc1`
ZINC134079	0.611	242.2 Da LogP 2.75 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(C(=O)O)cc2)cc1`
ZINC1640789	0.611	374.3 Da LogP 3.55 TPSA 108.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccc(C(=O)c3ccc(C(=O)O)cc3)cc…`
ZINC2146859	0.611	270.2 Da LogP 2.31 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC3147211	0.611	318.3 Da LogP 4.42 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(-c3ccc(C(=O)O)cc3)cc2)cc1`
ZINC2539781	0.600	382.1 Da LogP 4.24 TPSA 34.1	✓ Ro5	✓ Clean	`O=C(c1ccccc1)C(Br)(Br)C(=O)c1ccccc1`
ZINC100029384	0.594	244.1 Da LogP -2.23 TPSA 144.5	✓ Ro5	✓ Clean	`C[C@H](O)[C@@H](O)[C@@H](O)C(=O)COP(=O)(O)O`
ZINC4831627	0.593	370.5 Da LogP -0.21 TPSA 76.0	✓ Ro5	✓ Clean	`O=S(=O)(CC[n+]1ccccc1)CCS(=O)(=O)CC[n+]1ccccc1`
ZINC100009533	0.591	226.2 Da LogP 3.80 TPSA 62.0	✓ Ro5	Alert	`O=C(O)c1ccc(/N=N\c2ccccc2)cc1`
ZINC1601737	0.591	213.2 Da LogP 3.13 TPSA 49.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Nc2ccccc2)cc1`
ZINC1697492	0.591	212.2 Da LogP 2.98 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Cc2ccccc2)cc1`
ZINC169818652	0.591	380.5 Da LogP 2.76 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc([Si](c2ccccc2)(c2ccccc2)c2ccccc2)cc1`
ZINC33759110	0.591	224.3 Da LogP 3.56 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(/C=C/c2ccccc2)cc1`
ZINC346053	0.591	289.3 Da LogP 4.85 TPSA 40.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(N(c2ccccc2)c2ccccc2)cc1`
ZINC396612	0.591	230.3 Da LogP 3.54 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Sc2ccccc2)cc1`
ZINC409186	0.591	226.2 Da LogP 2.62 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1cccc(C(=O)c2ccccc2)c1`
ZINC409394	0.591	226.3 Da LogP 3.17 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(CCc2ccccc2)cc1`
ZINC4299335	0.591	222.2 Da LogP 2.78 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C#Cc2ccccc2)cc1`
ZINC4403618	0.591	226.2 Da LogP 3.80 TPSA 62.0	✓ Ro5	Alert	`O=C(O)c1ccc(/N=N/c2ccccc2)cc1`
ZINC4802802	0.591	288.3 Da LogP 4.57 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(c2ccccc2)c2ccccc2)cc1`
ZINC5538754	0.591	304.3 Da LogP 3.67 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(O)(c2ccccc2)c2ccccc2)cc1`
ZINC60939	0.591	214.2 Da LogP 3.18 TPSA 46.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2ccccc2)cc1`

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.