Protein profile

VK055_3220

glutamate racemase

Genome: KpATCC43816

Gene: AIK81781.1 murI Structure source: AlphaFold + ColabFold UniProt A0A0H3GLI1

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Amino acids 260

Annotations 8

Features 20

PDB binders 3

Druggability 0.59

Overview

Basic information about this protein and its source genome.

Accession: VK055_3220
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK81781.1 murI
Status: annotated
Amino acids: 260
Structure source: AlphaFold + ColabFold

5.1.1.3

GO:0006807 OBSOLETE. The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen. GO:0008881 Catalysis of the reaction: L-glutamate = D-glutamate. GO:0036361 OBSOLETE. Catalysis of the interconversion of the two enantiomers of a chiral amino acid or amino acid derivative. GO:0016855 Catalysis of a reaction that alters the configuration of one or more chiral centers in an amino acid. GO:0071555 A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. GO:0009252 The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls and consisting of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.

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 (%): 88.372
DEG E-value: 9.35e-162
Localization: Cytoplasmic
ColabFold pLDDT: 96.55

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 0.59

Structure A0A0H3GLI1

Pocket Pocket 2

P2Rank 0.304

Structure A0A0H3GLI1

Pocket Pocket 1

ColabFold model

FPocket 0.876 · Pocket 1

P2Rank 0.284 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 129 / 4744 genomes with a hit

Normalized 0.027

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

5.1.1.3

Gene Ontology (GO)

GO:0006807 OBSOLETE. The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
GO:0008881 Catalysis of the reaction: L-glutamate = D-glutamate.
GO:0036361 OBSOLETE. Catalysis of the interconversion of the two enantiomers of a chiral amino acid or amino acid derivative.
GO:0016855 Catalysis of a reaction that alters the configuration of one or more chiral centers in an amino acid.
GO:0071555 A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
GO:0009252 The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls and consisting of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.
GO:0008360 Any process that modulates the surface configuration of a cell.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records

Show feature table

Start	End	DB	Term	Name
66	74	ProSitePatterns	PS00923	Aspartate and glutamate racemases signature 1.
66	74	InterPro	IPR018187	Asp/Glu racemase, active site 1
3	219	PANTHER	PTHR21198	GLUTAMATE RACEMASE
9	211	Pfam	PF01177	Asp/Glu/Hydantoin racemase
9	211	InterPro	IPR015942	Asp/Glu/hydantoin racemase
104	256	SUPERFAMILY	SSF53681	Aspartate/glutamate racemase
104	256	InterPro	IPR001920	Asp/Glu racemase
2	102	SUPERFAMILY	SSF53681	Aspartate/glutamate racemase
2	102	InterPro	IPR001920	Asp/Glu racemase
177	187	ProSitePatterns	PS00924	Aspartate and glutamate racemases signature 2.
177	187	InterPro	IPR033134	Asp/Glu racemase, active site 2
1	145	FunFam	G3DSA:3.40.50.1860:FF:000002	Glutamate racemase
1	251	Hamap	MF_00258	Glutamate racemase [murI].
1	251	InterPro	IPR004391	Glutamate racemase
3	241	Gene3D	G3DSA:3.40.50.1860	-
3	241	InterPro	IPR001920	Asp/Glu racemase
2	246	NCBIfam	TIGR00067	glutamate racemase
2	246	InterPro	IPR004391	Glutamate racemase
91	204	Gene3D	G3DSA:3.40.50.1860	-
91	204	InterPro	IPR001920	Asp/Glu racemase

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_A0A0H3GLI1	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_3220	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
5				0.237
7				0.027
1				0.004
4				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	7.02	0.304
2	6.35	0.266
3	1.67	0.023
4	1.6	0.021
5	1.3	0.012

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				0.023
2				0.0
4				0.0
11				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	6.64	0.284
2	6.46	0.273
3	0.99	0.005

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.

57 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
C2N	6DLI	Q5SHT7	123.5 Da LogP -0.36 TPSA 63.3	✓ Ro5	✓ Clean	`C([C@H](C(=O)O)N)Cl`
DGN	1B74	P56868	146.1 Da LogP -1.34 TPSA 106.4	✓ Ro5	✓ Clean	`C(CC(=O)N)[C@H](C(=O)O)N`
SIN	3IST	Q8Y7N7	118.1 Da LogP -0.06 TPSA 74.6	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL435982	Q03469	7.80	287.3 Da LogP 1.89 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](C[C@H](Cc1ccc2ccccc2c1)C(=O)O)C(=O)O`
CHEMBL452090	Q836J0	6.19	426.3 Da LogP 3.31 TPSA 106.7	✓ Ro5	✓ Clean	`CCCCSc1nc(N)c2[nH]c(=O)c(=O)n(Cc3ccc(Cl)c(Cl)c3…`
CHEMBL462555	Q836J0	6.05	389.5 Da LogP 2.60 TPSA 92.7	✓ Ro5	✓ Clean	`CCCCSc1nc(NC)c2[nH]c(=O)c(=O)n(Cc3ccc(F)cc3)c2n1`
CHEMBL502762	Q836J0	6.00	368.8 Da LogP 4.70 TPSA 43.6	✓ Ro5	✓ Clean	`CCCCSc1ncc2ncn(Cc3c(F)ccc(Cl)c3F)c2n1`

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
ZINC12650333	1.000	287.3 Da LogP 1.89 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](C[C@H](Cc1ccc2ccccc2c1)C(=O)O)C(=O)O`
ZINC12650337	1.000	287.3 Da LogP 1.89 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](C[C@@H](Cc1ccc2ccccc2c1)C(=O)O)C(=O)O`
ZINC19969	1.000	287.3 Da LogP 1.89 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](C[C@@H](Cc1ccc2ccccc2c1)C(=O)O)C(=O)O`
ZINC4655025	0.667	258.3 Da LogP 2.56 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)C[C@H](Cc1ccc2ccccc2c1)C(=O)O`
ZINC4655026	0.667	258.3 Da LogP 2.56 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)C[C@@H](Cc1ccc2ccccc2c1)C(=O)O`
ZINC2390999	0.655	275.3 Da LogP -1.99 TPSA 172.8	✓ Ro5	✓ Clean	`NC(=O)CC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC1529497	0.615	230.3 Da LogP 3.06 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCC(=O)O`
ZINC1531045	0.615	202.2 Da LogP 2.28 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)O`
ZINC1593115	0.615	216.3 Da LogP 2.67 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCC(=O)O`
ZINC1700020	0.615	244.3 Da LogP 3.45 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCC(=O)O`
ZINC34579977	0.615	214.3 Da LogP 1.19 TPSA 69.1	✓ Ro5	✓ Clean	`NC(=O)[C@@H](N)Cc1ccc2ccccc2c1`
ZINC3860440	0.615	258.4 Da LogP 3.84 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCC(=O)O`
ZINC3861298	0.615	286.4 Da LogP 4.62 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCC(=O)O`
ZINC5113062	0.615	272.4 Da LogP 4.23 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCC(=O)O`
ZINC33975567	0.590	216.2 Da LogP 1.83 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)[C@@H](O)Cc1ccc2ccccc2c1`
ZINC13491563	0.587	313.4 Da LogP 2.75 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](C[C@H](C/C=C/c1ccc2ccccc2c1)C(=O)O)C(=O)O`
ZINC1545895	0.587	313.4 Da LogP 2.75 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](C[C@@H](C/C=C/c1ccc2ccccc2c1)C(=O)O)C(=…`
ZINC78938452	0.587	313.4 Da LogP 2.75 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](C[C@H](C/C=C/c1ccc2ccccc2c1)C(=O)O)C(=O…`
ZINC78938460	0.587	313.4 Da LogP 2.75 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](C[C@@H](C/C=C/c1ccc2ccccc2c1)C(=O)O)C(=O…`
ZINC2391099	0.586	274.3 Da LogP -2.59 TPSA 178.6	✓ Ro5	✓ Clean	`NC(=O)CC[C@H](N)C(=O)N[C@@H](CCC(N)=O)C(=O)O`
ZINC2385840	0.585	229.3 Da LogP 2.18 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](CC(=O)O)Cc1ccc2ccccc2c1`
ZINC2385964	0.585	229.3 Da LogP 2.18 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](CC(=O)O)Cc1ccc2ccccc2c1`
ZINC2392303	0.581	305.4 Da LogP 3.45 TPSA 52.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc2ccccc2c1)C(=O)OCc1ccccc1`
ZINC34309984	0.581	305.4 Da LogP 3.45 TPSA 52.3	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc2ccccc2c1)C(=O)OCc1ccccc1`
ZINC23640481	0.571	229.3 Da LogP 1.88 TPSA 52.3	✓ Ro5	✓ Clean	`COC(=O)[C@@H](N)Cc1ccc2ccccc2c1`
ZINC23640484	0.571	229.3 Da LogP 1.88 TPSA 52.3	✓ Ro5	✓ Clean	`COC(=O)[C@H](N)Cc1ccc2ccccc2c1`
ZINC2556600	0.567	217.2 Da LogP -1.83 TPSA 135.5	✓ Ro5	✓ Clean	`C[C@H](NC(=O)[C@@H](N)CCC(N)=O)C(=O)O`
ZINC95970704	0.565	285.3 Da LogP 2.61 TPSA 66.4	✓ Ro5	✓ Clean	`CCC(=O)NC[C@@H](Cc1ccc2ccccc2c1)C(=O)O`
ZINC95970705	0.565	285.3 Da LogP 2.61 TPSA 66.4	✓ Ro5	✓ Clean	`CCC(=O)NC[C@H](Cc1ccc2ccccc2c1)C(=O)O`
ZINC1572706	0.563	260.2 Da LogP -1.05 TPSA 132.8	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)NCCNC(=O)CCC(=O)O`
ZINC238152494	0.563	323.4 Da LogP 3.17 TPSA 66.4	✓ Ro5	✓ Clean	`O=C(NC[C@@H](Cc1ccc2ccccc2c1)C(=O)O)C1CC=CC1`
ZINC262707988	0.563	323.4 Da LogP 3.17 TPSA 66.4	✓ Ro5	✓ Clean	`O=C(NC[C@H](Cc1ccc2ccccc2c1)C(=O)O)C1CC=CC1`
ZINC89064363	0.561	276.3 Da LogP 4.25 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)[C@H](Cc1ccc2ccccc2c1)c1ccccc1`
ZINC89064364	0.561	276.3 Da LogP 4.25 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)[C@@H](Cc1ccc2ccccc2c1)c1ccccc1`
ZINC12650594	0.558	305.3 Da LogP 1.75 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](C[C@H](Cc1ccc(C(F)(F)F)cc1)C(=O)O)C(=O)O`
ZINC4284312	0.556	272.3 Da LogP 2.65 TPSA 63.6	✓ Ro5	✓ Clean	`COC(=O)[C@H](CC(=O)O)Cc1ccc2ccccc2c1`
ZINC1581634	0.552	203.2 Da LogP -2.22 TPSA 135.5	✓ Ro5	✓ Clean	`NC(=O)CC[C@H](N)C(=O)NCC(=O)O`
ZINC5500823	0.552	203.2 Da LogP -2.22 TPSA 135.5	✓ Ro5	✓ Clean	`NC(=O)CC[C@@H](N)C(=O)NCC(=O)O`
ZINC12650469	0.545	238.2 Da LogP 0.13 TPSA 113.5	✓ Ro5	✓ Clean	`N[C@@H](C[C@H](Cc1cccnc1)C(=O)O)C(=O)O`
ZINC20579509	0.545	243.3 Da LogP 2.13 TPSA 52.3	✓ Ro5	✓ Clean	`COC(=O)[C@@H](CN)Cc1ccc2ccccc2c1`
ZINC20579512	0.545	243.3 Da LogP 2.13 TPSA 52.3	✓ Ro5	✓ Clean	`COC(=O)[C@H](CN)Cc1ccc2ccccc2c1`
ZINC80169752	0.543	348.4 Da LogP 4.22 TPSA 63.6	✓ Ro5	✓ Clean	`O=C(O)C[C@H](Cc1ccc2ccccc2c1)C(=O)OCc1ccccc1`
ZINC80169754	0.543	348.4 Da LogP 4.22 TPSA 63.6	✓ Ro5	✓ Clean	`O=C(O)C[C@@H](Cc1ccc2ccccc2c1)C(=O)OCc1ccccc1`
ZINC143569799	0.533	271.4 Da LogP 3.05 TPSA 52.3	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)[C@@H](N)Cc1ccc2ccccc2c1`
ZINC1703342	0.533	202.2 Da LogP 1.07 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCC(=O)CCCC(=O)O`
ZINC1728397	0.533	233.2 Da LogP -0.29 TPSA 115.1	✓ Ro5	✓ Clean	`O=C(O)CCN(CCC(=O)O)CCC(=O)O`
ZINC2508031	0.533	230.3 Da LogP 1.85 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCC(=O)CCCCC(=O)O`
ZINC2517013	0.533	250.2 Da LogP 0.89 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)CCP(CCC(=O)O)CCC(=O)O`
ZINC71610464	0.532	329.4 Da LogP 2.75 TPSA 89.6	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)[C@@H](C(=O)O)[C@H](N)Cc1ccc2cccc…`
ZINC71610470	0.532	329.4 Da LogP 2.75 TPSA 89.6	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)[C@@H](C(=O)O)[C@@H](N)Cc1ccc2ccc…`

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.