Protein profile

VK055_4106

arginine decarboxylase

Genome: KpATCC43816

Gene: speA AIK82652.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GT44

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Amino acids 632

Annotations 7

Features 62

PDB binders 4

Druggability 0.639

Overview

Basic information about this protein and its source genome.

Accession: VK055_4106
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: speA AIK82652.1
Status: annotated
Amino acids: 632
Structure source: AlphaFold + ColabFold

4.1.1.19

GO:0008295 The chemical reactions and pathways resulting in the formation of spermidine, N-(3-aminopropyl)-1,4-diaminobutane. GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GO:0008792 Catalysis of the reaction: L-arginine + H+ = agmatine + CO2. GO:0006527 The chemical reactions and pathways resulting in the breakdown of L-arginine. GO:0046872 Binding to a metal ion. GO:0033388 The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane, from other compounds, including arginine.

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 (%): 44.462
DEG E-value: 0.0
Localization: Periplasmic
ColabFold pLDDT: 92.61

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 0.639

Structure A0A0H3GT44

Pocket Pocket 9

P2Rank 0.886

Structure A0A0H3GT44

Pocket Pocket 1

ColabFold model

FPocket 0.757 · Pocket 2

P2Rank 0.859 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 132 / 4744 genomes with a hit

Normalized 0.028

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

4.1.1.19

Gene Ontology (GO)

GO:0008295 The chemical reactions and pathways resulting in the formation of spermidine, N-(3-aminopropyl)-1,4-diaminobutane.
GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
GO:0008792 Catalysis of the reaction: L-arginine + H+ = agmatine + CO2.
GO:0006527 The chemical reactions and pathways resulting in the breakdown of L-arginine.
GO:0046872 Binding to a metal ion.
GO:0033388 The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane, from other compounds, including arginine.

Sequence Features

Domain/signature hits from InterPro and related databases.

62 records

Show feature table

Start	End	DB	Term	Name
74	341	Pfam	PF02784	Pyridoxal-dependent decarboxylase, pyridoxal binding domain
74	341	InterPro	IPR022644	Orn/DAP/Arg decarboxylase 2, N-terminal
455	558	SUPERFAMILY	SSF50621	Alanine racemase C-terminal domain-like
455	558	InterPro	IPR009006	Alanine racemase/group IV decarboxylase, C-terminal
4	631	PANTHER	PTHR43295	ARGININE DECARBOXYLASE
4	631	InterPro	IPR002985	Arginine decarboxylase
579	632	FunFam	G3DSA:1.10.287.3440:FF:000001	Biosynthetic arginine decarboxylase
487	512	PRINTS	PR01180	Arginine decarboxylase signature
487	512	InterPro	IPR002985	Arginine decarboxylase
90	104	PRINTS	PR01180	Arginine decarboxylase signature
90	104	InterPro	IPR002985	Arginine decarboxylase
194	216	PRINTS	PR01180	Arginine decarboxylase signature
194	216	InterPro	IPR002985	Arginine decarboxylase
321	338	PRINTS	PR01180	Arginine decarboxylase signature
321	338	InterPro	IPR002985	Arginine decarboxylase
170	191	PRINTS	PR01180	Arginine decarboxylase signature
170	191	InterPro	IPR002985	Arginine decarboxylase
462	483	PRINTS	PR01180	Arginine decarboxylase signature
462	483	InterPro	IPR002985	Arginine decarboxylase
144	159	PRINTS	PR01180	Arginine decarboxylase signature
144	159	InterPro	IPR002985	Arginine decarboxylase
540	561	PRINTS	PR01180	Arginine decarboxylase signature
540	561	InterPro	IPR002985	Arginine decarboxylase
66	81	PRINTS	PR01180	Arginine decarboxylase signature
66	81	InterPro	IPR002985	Arginine decarboxylase
66	343	SUPERFAMILY	SSF51419	PLP-binding barrel
66	343	InterPro	IPR029066	PLP-binding barrel
56	561	CDD	cd06830	PLPDE_III_ADC
56	561	InterPro	IPR002985	Arginine decarboxylase
446	566	FunFam	G3DSA:2.40.37.10:FF:000001	Biosynthetic arginine decarboxylase
360	455	FunFam	G3DSA:1.20.58.930:FF:000001	Biosynthetic arginine decarboxylase
98	116	PRINTS	PR01179	Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature
98	116	InterPro	IPR000183	Ornithine/DAP/Arg decarboxylase
331	350	PRINTS	PR01179	Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature
331	350	InterPro	IPR000183	Ornithine/DAP/Arg decarboxylase
120	132	PRINTS	PR01179	Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature
120	132	InterPro	IPR000183	Ornithine/DAP/Arg decarboxylase
540	553	PRINTS	PR01179	Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature
540	553	InterPro	IPR000183	Ornithine/DAP/Arg decarboxylase
237	250	PRINTS	PR01179	Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature
237	250	InterPro	IPR000183	Ornithine/DAP/Arg decarboxylase
67	343	FunFam	G3DSA:3.20.20.10:FF:000001	Biosynthetic arginine decarboxylase
67	343	Gene3D	G3DSA:3.20.20.10	Alanine racemase
67	343	InterPro	IPR029066	PLP-binding barrel
360	455	Gene3D	G3DSA:1.20.58.930	-
5	630	NCBIfam	TIGR01273	arginine decarboxylase
5	630	InterPro	IPR002985	Arginine decarboxylase
13	566	Gene3D	G3DSA:2.40.37.10	Lyase, Ornithine Decarboxylase; Chain A, domain 1
13	566	InterPro	IPR009006	Alanine racemase/group IV decarboxylase, C-terminal
1	632	PIRSF	PIRSF001336	ARGDC
1	632	InterPro	IPR002985	Arginine decarboxylase
580	629	Pfam	PF17944	Arginine decarboxylase C-terminal helical extension
580	629	InterPro	IPR041128	Arginine decarboxylase, C-terminal helical
2	631	Hamap	MF_01417	Biosynthetic arginine decarboxylase [speA].
2	631	InterPro	IPR002985	Arginine decarboxylase
275	288	ProSitePatterns	PS00879	Orn/DAP/Arg decarboxylases family 2 signature 2.
275	288	InterPro	IPR022657	Orn/DAP/Arg decarboxylase 2, conserved site
579	632	Gene3D	G3DSA:1.10.287.3440	-
366	452	Pfam	PF17810	Arginine decarboxylase helical bundle domain
366	452	InterPro	IPR040634	Arginine decarboxylase, helical bundle domain
98	116	ProSitePatterns	PS00878	Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site.
98	116	InterPro	IPR022653	Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site

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_A0A0H3GT44	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_4106	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
3				0.002
43				0.002
1				0.0
7				0.0

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	27.93	0.886
2	11.95	0.547
3	2.65	0.063
4	2.39	0.052
5	1.74	0.026

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
5				0.001
44				0.001
6				0.0
10				0.0

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	24.88	0.859
2	10.74	0.495
3	2.79	0.069
4	1.18	0.009
5	1.15	0.008

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.

54 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
AG2	3N2O	Q7MK24	130.2 Da LogP -0.79 TPSA 87.9	✓ Ro5	✓ Clean	`C(CCNC(=N)N)CN`
AZ1	1TUF	Q58497	188.2 Da LogP 1.89 TPSA 74.6	✓ Ro5	✓ Clean	`C(CCCC(=O)O)CCCC(=O)O`
LLP	4XG1	A1SR00	375.3 Da LogP 0.71 TPSA 175.6	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/CCCCC(C(=O)O)N)O`
TME	4XG1	A1SR00	44.1 Da LogP 1.42 TPSA 0.0	✓ Ro5	✓ Clean	`CCC`

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
ZINC1529497	1.000	230.3 Da LogP 3.06 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCC(=O)O`
ZINC1531045	1.000	202.2 Da LogP 2.28 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)O`
ZINC1593115	1.000	216.3 Da LogP 2.67 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCC(=O)O`
ZINC1700020	1.000	244.3 Da LogP 3.45 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCC(=O)O`
ZINC3860440	1.000	258.4 Da LogP 3.84 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCC(=O)O`
ZINC3861298	1.000	286.4 Da LogP 4.62 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCC(=O)O`
ZINC5113062	1.000	272.4 Da LogP 4.23 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCC(=O)O`
ZINC26897400	0.800	286.4 Da LogP 3.41 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCC(=O)CCCCCCC(=O)O`
ZINC3074813	0.800	258.3 Da LogP 2.63 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCC(=O)CCCCCC(=O)O`
ZINC34423725	0.800	342.5 Da LogP 4.97 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)CCCCCCCCC(=O)O`
ZINC4822898	0.800	272.3 Da LogP 3.02 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCC(=O)CCCCCC(=O)O`
ZINC4822900	0.800	300.4 Da LogP 3.80 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)CCCCCC(=O)O`
ZINC13433578	0.750	201.3 Da LogP 1.68 TPSA 80.4	✓ Ro5	✓ Clean	`NC(=O)CCCCCCCCC(=O)O`
ZINC14510370	0.750	244.4 Da LogP 3.74 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCO`
ZINC1531061	0.750	216.3 Da LogP 2.96 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCO`
ZINC1610426	0.750	230.3 Da LogP 3.35 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCO`
ZINC2168567	0.750	202.3 Da LogP 2.57 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCO`
ZINC3074815	0.750	230.3 Da LogP 1.85 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCC(=O)CCCC(=O)O`
ZINC3861297	0.750	272.4 Da LogP 4.52 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCCO`
ZINC4284502	0.750	258.4 Da LogP 4.13 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCO`
ZINC5287109	0.750	286.5 Da LogP 4.91 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCCCO`
ZINC13545924	0.737	214.3 Da LogP -0.10 TPSA 123.8	1 viol.	✓ Clean	`N=C(N)NCCCCCCCNC(=N)N`
ZINC1561855	0.737	200.3 Da LogP -0.49 TPSA 123.8	1 viol.	✓ Clean	`N=C(N)NCCCCCCNC(=N)N`
ZINC2013578	0.737	228.3 Da LogP 0.29 TPSA 123.8	1 viol.	✓ Clean	`N=C(N)NCCCCCCCCNC(=N)N`
ZINC3995661	0.737	256.4 Da LogP 1.07 TPSA 123.8	1 viol.	✓ Clean	`N=C(N)NCCCCCCCCCCNC(=N)N`
ZINC2508031	0.733	230.3 Da LogP 1.85 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCC(=O)CCCCC(=O)O`
ZINC2114966	0.724	332.2 Da LogP 0.99 TPSA 149.5	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(/C=N/CCCC(=O)O)c1O`
ZINC12954423	0.706	232.4 Da LogP 3.90 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCS`
ZINC13357569	0.706	243.4 Da LogP 3.71 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCC(=O)O`
ZINC138216182	0.706	293.2 Da LogP 4.76 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCBr`
ZINC14619253	0.706	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCCC(=O)O`
ZINC1529498	0.706	200.3 Da LogP 3.99 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)O`
ZINC1530417	0.706	228.4 Da LogP 4.77 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)O`
ZINC1628119	0.706	214.3 Da LogP 4.38 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)O`
ZINC1763117	0.706	201.3 Da LogP 2.54 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCC(=O)O`
ZINC1841307	0.706	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCCCC(=O)O`
ZINC1845814	0.706	215.3 Da LogP 2.93 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCCC(=O)O`
ZINC1845839	0.706	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCC(=O)O`
ZINC2164257	0.706	218.4 Da LogP 3.51 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCS`
ZINC22048354	0.706	229.4 Da LogP 3.32 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCC(=O)O`
ZINC33822328	0.706	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCCCCCCC(=O)O`
ZINC34552398	0.706	257.4 Da LogP 4.10 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCC(=O)O`
ZINC34628306	0.706	271.4 Da LogP 4.49 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCCC(=O)O`
ZINC35465466	0.706	244.3 Da LogP 2.24 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCC(=O)CCC(=O)O`
ZINC5855130	0.706	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCCCCC(=O)O`
ZINC90745150	0.706	260.4 Da LogP 4.68 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCS`
ZINC4789573	0.667	310.4 Da LogP 4.62 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCC#CCCCCCCCC(=O)O`
ZINC5501162	0.667	350.5 Da LogP 4.52 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCSCCCCCCSCCCCC(=O)O`
ZINC13742471	0.636	299.5 Da LogP 0.66 TPSA 135.8	1 viol.	✓ Clean	`N=C(N)NCCCCCCNCCCCCCNC(=N)N`
ZINC5015111	0.636	229.3 Da LogP -1.29 TPSA 135.8	1 viol.	✓ Clean	`N=C(N)NCCCCNCCCNC(=N)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.