Protein profile

KP13_02723

Biosynthetic arginine decarboxylase

Genome: KpKP13

Gene: AHE42709.1 speA Structure source: AlphaFold + ColabFold UniProt A0A0H3GT44

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Amino acids 637

Annotations 7

Features 62

PDB binders 4

Druggability 0.639

Overview

Basic information about this protein and its source genome.

Accession: KP13_02723
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE42709.1 speA
Status: annotated
Amino acids: 637
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:0008792 Catalysis of the reaction: L-arginine + H+ = agmatine + CO2. 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: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: 92.09

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 0.834 · Pocket 19

P2Rank 0.83 · 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:0008792 Catalysis of the reaction: L-arginine + H+ = agmatine + CO2.
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: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
103	121	ProSitePatterns	PS00878	Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site.
103	121	InterPro	IPR022653	Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site
1	637	PIRSF	PIRSF001336	ARGDC
1	637	InterPro	IPR002985	Arginine decarboxylase
584	637	Gene3D	G3DSA:1.10.287.3440	-
18	571	Gene3D	G3DSA:2.40.37.10	Lyase, Ornithine Decarboxylase; Chain A, domain 1
18	571	InterPro	IPR009006	Alanine racemase/group IV decarboxylase, C-terminal
451	571	FunFam	G3DSA:2.40.37.10:FF:000001	Biosynthetic arginine decarboxylase
10	635	NCBIfam	TIGR01273	arginine decarboxylase
10	635	InterPro	IPR002985	Arginine decarboxylase
371	457	Pfam	PF17810	Arginine decarboxylase helical bundle domain
371	457	InterPro	IPR040634	Arginine decarboxylase, helical bundle domain
365	460	Gene3D	G3DSA:1.20.58.930	-
72	348	Gene3D	G3DSA:3.20.20.10	Alanine racemase
72	348	InterPro	IPR029066	PLP-binding barrel
584	637	FunFam	G3DSA:1.10.287.3440:FF:000001	Biosynthetic arginine decarboxylase
72	348	FunFam	G3DSA:3.20.20.10:FF:000001	Biosynthetic arginine decarboxylase
585	634	Pfam	PF17944	Arginine decarboxylase C-terminal helical extension
585	634	InterPro	IPR041128	Arginine decarboxylase, C-terminal helical
79	346	Pfam	PF02784	Pyridoxal-dependent decarboxylase, pyridoxal binding domain
79	346	InterPro	IPR022644	Orn/DAP/Arg decarboxylase 2, N-terminal
61	566	CDD	cd06830	PLPDE_III_ADC
61	566	InterPro	IPR002985	Arginine decarboxylase
460	563	SUPERFAMILY	SSF50621	Alanine racemase C-terminal domain-like
460	563	InterPro	IPR009006	Alanine racemase/group IV decarboxylase, C-terminal
71	348	SUPERFAMILY	SSF51419	PLP-binding barrel
71	348	InterPro	IPR029066	PLP-binding barrel
7	636	Hamap	MF_01417	Biosynthetic arginine decarboxylase [speA].
7	636	InterPro	IPR002985	Arginine decarboxylase
6	636	PANTHER	PTHR43295	ARGININE DECARBOXYLASE
6	636	InterPro	IPR002985	Arginine decarboxylase
280	293	ProSitePatterns	PS00879	Orn/DAP/Arg decarboxylases family 2 signature 2.
280	293	InterPro	IPR022657	Orn/DAP/Arg decarboxylase 2, conserved site
103	121	PRINTS	PR01179	Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature
103	121	InterPro	IPR000183	Ornithine/DAP/Arg decarboxylase
545	558	PRINTS	PR01179	Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature
545	558	InterPro	IPR000183	Ornithine/DAP/Arg decarboxylase
336	355	PRINTS	PR01179	Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature
336	355	InterPro	IPR000183	Ornithine/DAP/Arg decarboxylase
125	137	PRINTS	PR01179	Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature
125	137	InterPro	IPR000183	Ornithine/DAP/Arg decarboxylase
242	255	PRINTS	PR01179	Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature
242	255	InterPro	IPR000183	Ornithine/DAP/Arg decarboxylase
71	86	PRINTS	PR01180	Arginine decarboxylase signature
71	86	InterPro	IPR002985	Arginine decarboxylase
492	517	PRINTS	PR01180	Arginine decarboxylase signature
492	517	InterPro	IPR002985	Arginine decarboxylase
95	109	PRINTS	PR01180	Arginine decarboxylase signature
95	109	InterPro	IPR002985	Arginine decarboxylase
175	196	PRINTS	PR01180	Arginine decarboxylase signature
175	196	InterPro	IPR002985	Arginine decarboxylase
149	164	PRINTS	PR01180	Arginine decarboxylase signature
149	164	InterPro	IPR002985	Arginine decarboxylase
199	221	PRINTS	PR01180	Arginine decarboxylase signature
199	221	InterPro	IPR002985	Arginine decarboxylase
467	488	PRINTS	PR01180	Arginine decarboxylase signature
467	488	InterPro	IPR002985	Arginine decarboxylase
545	566	PRINTS	PR01180	Arginine decarboxylase signature
545	566	InterPro	IPR002985	Arginine decarboxylase
326	343	PRINTS	PR01180	Arginine decarboxylase signature
326	343	InterPro	IPR002985	Arginine decarboxylase
365	460	FunFam	G3DSA:1.20.58.930:FF:000001	Biosynthetic arginine decarboxylase

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 KP13_02723	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
9				0.639

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	19.81	0.845
2	5.25	0.245
3	1.67	0.028
4	1.2	0.011
5	0.74	0.002

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
19				0.834

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	15.22	0.749
2	3.16	0.108
3	2.05	0.045
4	1.14	0.009

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.