Protein profile

VK055_1138

L-Ala-D/L-Glu epimerase, a muconate lactonizing enzyme L-Ala-D/L-Glu epimerase

Genome: KpATCC43816

Gene: AIK79762.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GNH7

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Amino acids 321

Annotations 4

Features 24

PDB binders 4

Druggability 0.931

Overview

Basic information about this protein and its source genome.

Accession: VK055_1138
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK79762.1
Status: annotated
Amino acids: 321
Structure source: AlphaFold + ColabFold

5.1.1.-

GO:0009063 The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents. GO:0016855 Catalysis of a reaction that alters the configuration of one or more chiral centers in an amino acid. GO:0046872 Binding to a metal ion.

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 (%): 27.616
Localization: Cytoplasmic
ColabFold pLDDT: 97.96

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 0.931

Structure A0A0H3GNH7

Pocket Pocket 1

P2Rank 0.865

Structure A0A0H3GNH7

Pocket Pocket 1

ColabFold model

FPocket 0.87 · Pocket 1

P2Rank 0.742 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 90 / 4744 genomes with a hit

Normalized 0.019

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

5.1.1.-

Gene Ontology (GO)

GO:0009063 The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents.
GO:0016855 Catalysis of a reaction that alters the configuration of one or more chiral centers in an amino acid.
GO:0046872 Binding to a metal ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

24 records

Show feature table

Start	End	DB	Term	Name
115	321	Gene3D	G3DSA:3.20.20.120	-
115	321	InterPro	IPR036849	Enolase-like, C-terminal domain superfamily
1	103	FunFam	G3DSA:3.30.390.10:FF:000010	Dipeptide epimerase
2	112	Pfam	PF02746	Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
2	112	InterPro	IPR013341	Mandelate racemase/muconate lactonizing enzyme, N-terminal domain
19	317	PANTHER	PTHR48080	D-GALACTONATE DEHYDRATASE-RELATED
19	317	InterPro	IPR034593	D-galactonate dehydratase DgoD-like
10	321	SFLD	SFLDF00010	dipeptide epimerase
10	321	InterPro	IPR034603	Dipeptide epimerase
130	223	SMART	SM00922	MR_MLE_2
130	223	InterPro	IPR013342	Mandelate racemase/muconate lactonizing enzyme, C-terminal
3	304	CDD	cd03319	L-Ala-DL-Glu_epimerase
3	304	InterPro	IPR034603	Dipeptide epimerase
1	104	Gene3D	G3DSA:3.30.390.10	-
1	104	InterPro	IPR029017	Enolase-like, N-terminal
133	319	Pfam	PF13378	Enolase C-terminal domain-like
133	319	InterPro	IPR029065	Enolase C-terminal domain-like
173	204	ProSitePatterns	PS00909	Mandelate racemase / muconate lactonizing enzyme family signature 2.
173	204	InterPro	IPR018110	Mandelate racemase/muconate lactonizing enzyme, conserved site
116	318	SUPERFAMILY	SSF51604	Enolase C-terminal domain-like
116	318	InterPro	IPR036849	Enolase-like, C-terminal domain superfamily
10	321	SFLD	SFLDS00001	Enolase
2	112	SUPERFAMILY	SSF54826	Enolase N-terminal domain-like
2	112	InterPro	IPR029017	Enolase-like, N-terminal

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_A0A0H3GNH7	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_1138	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
1				0.931

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	20.22	0.852
2	2.24	0.055
3	1.3	0.014

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
1				0.87
17				0.414

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	13.64	0.694
2	2.71	0.081
3	1.62	0.026
4	1.32	0.015

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
FUM	3R11	B0TZW0	116.1 Da LogP -0.29 TPSA 74.6	✓ Ro5	✓ Clean	`C(=C/C(=O)O)\C(=O)O`
NSK	2P8B	Q81IL5	246.3 Da LogP -0.45 TPSA 129.7	✓ Ro5	✓ Clean	`C(CCN)C[C@@H](C(=O)O)NC(=O)CCC(=O)O`
SUG	2P8C	Q81IL5	274.3 Da LogP -1.32 TPSA 165.6	1 viol.	✓ Clean	`C(C[C@@H](C(=O)O)NC(=O)CCC(=O)O)CNC(=N)N`
TAR	3R0U	B0TZW0	150.1 Da LogP -2.12 TPSA 115.1	✓ Ro5	✓ Clean	`[C@H]([C@@H](C(=O)O)O)(C(=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
ZINC1866114950	0.844	260.3 Da LogP -0.06 TPSA 129.7	✓ Ro5	✓ Clean	`NCCCC[C@H](NC(=O)CCCC(=O)O)C(=O)O`
ZINC1530138	0.806	217.3 Da LogP -0.97 TPSA 118.4	✓ Ro5	✓ Clean	`NCCCC[C@H](NC(=O)CCN)C(=O)O`
ZINC403598	0.800	273.3 Da LogP 2.14 TPSA 92.8	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(Oc2ccc(O)cc2)cc1)C(=O)O`
ZINC403599	0.800	273.3 Da LogP 2.14 TPSA 92.8	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(Oc2ccc(O)cc2)cc1)C(=O)O`
ZINC15261332	0.744	303.3 Da LogP -1.99 TPSA 191.6	1 viol.	✓ Clean	`N=C(N)NCCC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC39351856	0.741	328.4 Da LogP 1.26 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(-c2ccc(C[C@H](N)C(=O)O)cc2)cc1)C…`
ZINC1576211	0.730	231.3 Da LogP -2.22 TPSA 154.3	1 viol.	✓ Clean	`N=C(N)NCCC[C@H](NC(=O)CN)C(=O)O`
ZINC116981435	0.706	319.3 Da LogP -0.81 TPSA 179.0	1 viol.	✓ Clean	`NCCCC[C@@H](NC(=O)N[C@@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC116981437	0.706	319.3 Da LogP -0.81 TPSA 179.0	1 viol.	✓ Clean	`NCCCC[C@@H](NC(=O)N[C@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC116981440	0.706	319.3 Da LogP -0.81 TPSA 179.0	1 viol.	✓ Clean	`NCCCC[C@H](NC(=O)N[C@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC40860752	0.706	319.3 Da LogP -0.81 TPSA 179.0	1 viol.	✓ Clean	`NCCCC[C@H](NC(=O)N[C@@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC1847640	0.703	216.2 Da LogP -1.16 TPSA 128.3	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CCCNC(=N)N)C(=O)O`
ZINC2169795	0.703	216.2 Da LogP -1.16 TPSA 128.3	✓ Ro5	✓ Clean	`CC(=O)N[C@H](CCCNC(=N)N)C(=O)O`
ZINC1722125	0.694	217.2 Da LogP -1.63 TPSA 154.3	1 viol.	✓ Clean	`N=C(N)NCCC[C@H](NC(N)=O)C(=O)O`
ZINC4537126	0.694	217.2 Da LogP -1.63 TPSA 154.3	1 viol.	✓ Clean	`N=C(N)NCCC[C@@H](NC(N)=O)C(=O)O`
ZINC12359024	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)C(=O)O`
ZINC13533920	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC1532740	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC1549593	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC2013424	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC3581021	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC3860635	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)C(=O)O`
ZINC5783661	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(=O)O`
ZINC6072527	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC32333	0.690	244.1 Da LogP 1.40 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(Br)cc1)C(=O)O`
ZINC32334	0.690	244.1 Da LogP 1.40 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(Br)cc1)C(=O)O`
ZINC3679925	0.690	291.1 Da LogP 1.25 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(I)cc1)C(=O)O`
ZINC391104	0.690	291.1 Da LogP 1.25 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(I)cc1)C(=O)O`
ZINC4202286	0.690	209.2 Da LogP 0.34 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(C(=O)O)cc1)C(=O)O`
ZINC4202287	0.690	209.2 Da LogP 0.34 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(C(=O)O)cc1)C(=O)O`
ZINC6092920	0.690	223.2 Da LogP 0.27 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(CC(=O)O)cc1)C(=O)O`
ZINC6506146	0.690	223.2 Da LogP 0.27 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(CC(=O)O)cc1)C(=O)O`
ZINC34319489	0.688	231.3 Da LogP 1.50 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc2cc(O)ccc2c1)C(=O)O`
ZINC34319490	0.688	231.3 Da LogP 1.50 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc2cc(O)ccc2c1)C(=O)O`
ZINC1529261	0.684	304.3 Da LogP -1.39 TPSA 185.8	1 viol.	✓ Clean	`N=C(N)NCCC[C@@H](N[C@@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC1529262	0.684	304.3 Da LogP -1.39 TPSA 185.8	1 viol.	✓ Clean	`N=C(N)NCCC[C@@H](N[C@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC1529939	0.684	304.3 Da LogP -1.39 TPSA 185.8	1 viol.	✓ Clean	`N=C(N)NCCC[C@H](N[C@@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC1529940	0.684	304.3 Da LogP -1.39 TPSA 185.8	1 viol.	✓ Clean	`N=C(N)NCCC[C@H](N[C@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC1530510	0.684	246.3 Da LogP -1.23 TPSA 148.5	1 viol.	✓ Clean	`N=C(N)NCCC[C@H](NCCC(=O)O)C(=O)O`
ZINC1530296	0.677	247.2 Da LogP -0.71 TPSA 141.0	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)N[C@@H](CCC(=O)O)C(=O)O`
ZINC2512061	0.677	360.4 Da LogP 0.67 TPSA 167.1	1 viol.	✓ Clean	`N[C@@H](Cc1ccc(O)c(-c2cc(C[C@H](N)C(=O)O)ccc2O)…`
ZINC6091882	0.677	360.4 Da LogP 0.67 TPSA 167.1	1 viol.	✓ Clean	`N[C@@H](Cc1ccc(O)c(-c2cc(C[C@@H](N)C(=O)O)ccc2O…`
ZINC6091894	0.677	360.4 Da LogP 0.67 TPSA 167.1	1 viol.	✓ Clean	`N[C@H](Cc1ccc(O)c(-c2cc(C[C@@H](N)C(=O)O)ccc2O)…`
ZINC6783254	0.676	231.2 Da LogP 0.61 TPSA 103.7	✓ Ro5	✓ Clean	`CCCC[C@H](NC(=O)CCC(=O)O)C(=O)O`
ZINC6783285	0.676	231.2 Da LogP 0.61 TPSA 103.7	✓ Ro5	✓ Clean	`CCCC[C@@H](NC(=O)CCC(=O)O)C(=O)O`
ZINC113625226	0.676	272.4 Da LogP 2.05 TPSA 92.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)N[C@@H](CCCCN)C(=O)O`
ZINC28539131	0.676	328.5 Da LogP 3.61 TPSA 92.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)N[C@@H](CCCCN)C(=O)O`
ZINC14982778	0.667	207.2 Da LogP 0.84 TPSA 80.4	✓ Ro5	✓ Clean	`CC(=O)c1ccc(C[C@@H](N)C(=O)O)cc1`
ZINC14982780	0.667	207.2 Da LogP 0.84 TPSA 80.4	✓ Ro5	✓ Clean	`CC(=O)c1ccc(C[C@H](N)C(=O)O)cc1`
ZINC2575618	0.667	208.2 Da LogP -0.26 TPSA 106.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc(C[C@H](N)C(=O)O)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.