Protein profile

KP13_02267

Diaminopimelate decarboxylase

Genome: KpKP13

Gene: AHE42840.1 lysA Structure source: AlphaFold + ColabFold UniProt A0A0H3GSP6

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Amino acids 420

Annotations 5

Features 43

PDB binders 6

Druggability 0.265

Overview

Basic information about this protein and its source genome.

Accession: KP13_02267
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE42840.1 lysA
Status: annotated
Amino acids: 420
Structure source: AlphaFold + ColabFold

4.1.1.20

GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate. 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:0008836 Catalysis of the reaction: meso-2,6-diaminopimelate + H+ = L-lysine + CO2. GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 96.56

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 0.265

Structure A0A0H3GSP6

Pocket Pocket 10

P2Rank 0.912

Structure A0A0H3GSP6

Pocket Pocket 1

ColabFold model

FPocket 0.39 · Pocket 4

P2Rank 0.954 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 111 / 4744 genomes with a hit

Normalized 0.023

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

4.1.1.20

Gene Ontology (GO)

GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
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:0008836 Catalysis of the reaction: meso-2,6-diaminopimelate + H+ = L-lysine + CO2.
GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.

Sequence Features

Domain/signature hits from InterPro and related databases.

43 records

Show feature table

Start	End	DB	Term	Name
33	275	Pfam	PF02784	Pyridoxal-dependent decarboxylase, pyridoxal binding domain
33	275	InterPro	IPR022644	Orn/DAP/Arg decarboxylase 2, N-terminal
216	229	ProSitePatterns	PS00879	Orn/DAP/Arg decarboxylases family 2 signature 2.
216	229	InterPro	IPR022657	Orn/DAP/Arg decarboxylase 2, conserved site
25	277	SUPERFAMILY	SSF51419	PLP-binding barrel
25	277	InterPro	IPR029066	PLP-binding barrel
293	311	PRINTS	PR01181	Diaminopimelate decarboxylase signature
293	311	InterPro	IPR002986	Diaminopimelate decarboxylase, LysA
69	86	PRINTS	PR01181	Diaminopimelate decarboxylase signature
69	86	InterPro	IPR002986	Diaminopimelate decarboxylase, LysA
157	166	PRINTS	PR01181	Diaminopimelate decarboxylase signature
157	166	InterPro	IPR002986	Diaminopimelate decarboxylase, LysA
386	408	PRINTS	PR01181	Diaminopimelate decarboxylase signature
386	408	InterPro	IPR002986	Diaminopimelate decarboxylase, LysA
22	416	Gene3D	G3DSA:2.40.37.10	Lyase, Ornithine Decarboxylase; Chain A, domain 1
22	416	InterPro	IPR009006	Alanine racemase/group IV decarboxylase, C-terminal
12	416	PANTHER	PTHR43727	DIAMINOPIMELATE DECARBOXYLASE
33	279	Gene3D	G3DSA:3.20.20.10	Alanine racemase
33	279	InterPro	IPR029066	PLP-binding barrel
14	419	Hamap	MF_02120	Diaminopimelate decarboxylase [lysA].
14	419	InterPro	IPR002986	Diaminopimelate decarboxylase, LysA
8	418	NCBIfam	TIGR01048	diaminopimelate decarboxylase
8	418	InterPro	IPR002986	Diaminopimelate decarboxylase, LysA
33	279	FunFam	G3DSA:3.20.20.10:FF:000009	Diaminopimelate decarboxylase
276	376	Pfam	PF00278	Pyridoxal-dependent decarboxylase, C-terminal sheet domain
276	376	InterPro	IPR022643	Orn/DAP/Arg decarboxylase 2, C-terminal
24	397	CDD	cd06828	PLPDE_III_DapDC
24	397	InterPro	IPR002986	Diaminopimelate decarboxylase, LysA
51	69	ProSitePatterns	PS00878	Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site.
51	69	InterPro	IPR022653	Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site
274	416	FunFam	G3DSA:2.40.37.10:FF:000007	Diaminopimelate decarboxylase
250	419	SUPERFAMILY	SSF50621	Alanine racemase C-terminal domain-like
250	419	InterPro	IPR009006	Alanine racemase/group IV decarboxylase, C-terminal
376	389	PRINTS	PR01179	Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature
376	389	InterPro	IPR000183	Ornithine/DAP/Arg decarboxylase
51	69	PRINTS	PR01179	Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature
51	69	InterPro	IPR000183	Ornithine/DAP/Arg decarboxylase
71	83	PRINTS	PR01179	Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature
71	83	InterPro	IPR000183	Ornithine/DAP/Arg decarboxylase
265	284	PRINTS	PR01179	Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature
265	284	InterPro	IPR000183	Ornithine/DAP/Arg decarboxylase
182	195	PRINTS	PR01179	Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature
182	195	InterPro	IPR000183	Ornithine/DAP/Arg 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_A0A0H3GSP6	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02267	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
10				0.265

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	19.34	0.838
2	1.77	0.032
3	1.26	0.012
4	0.72	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
4				0.39
13				0.341

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	29.97	0.933
2	1.44	0.019
3	1.28	0.013
4	1.02	0.006

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.

56 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
AZ1	1TUF	Q58497	188.2 Da LogP 1.89 TPSA 74.6	✓ Ro5	✓ Clean	`C(CCCC(=O)O)CCCC(=O)O`
DN9	6KNK	A0A0H3JPF2	465.4 Da LogP -1.41 TPSA 235.8	1 viol.	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)CNCCNC(=O)C[C@](CC(=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`
N2P	5GJP	O50657	102.2 Da LogP 0.07 TPSA 52.0	✓ Ro5	✓ Clean	`C(CCN)CCN`
TME	4XG1	A1SR00	44.1 Da LogP 1.42 TPSA 0.0	✓ Ro5	✓ Clean	`CCC`
X3J	6KNK	A0A0H3JPF2	234.2 Da LogP -2.26 TPSA 150.0	✓ Ro5	✓ Clean	`C(CNC(=O)C[C@](CC(=O)O)(C(=O)O)O)N`

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`
ZINC1685531	1.000	200.4 Da LogP 2.80 TPSA 52.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCN`
ZINC1700020	1.000	244.3 Da LogP 3.45 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCC(=O)O`
ZINC34273707	1.000	256.5 Da LogP 4.37 TPSA 52.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCCCN`
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`
ZINC5178646	1.000	228.4 Da LogP 3.59 TPSA 52.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCN`
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`
ZINC14686440	0.759	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	0.759	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	0.759	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(=…`
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`
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`
ZINC3593496	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@@](O)(CC(=O)O)C(=O)O`

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.