Protein profile

KP13_00390

Alanine racemase, biosynthetic

Genome: KpKP13

Gene: alr AHE46872.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GGW4

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Amino acids 359

Annotations 8

Features 41

PDB binders 9

Druggability 0.551

Overview

Basic information about this protein and its source genome.

Accession: KP13_00390
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: alr AHE46872.1
Status: annotated
Amino acids: 359
Structure source: AlphaFold + ColabFold

5.1.1.1

GO:0006522 OBSOLETE. The chemical reactions and pathways involving alanine, 2-aminopropanoic acid. GO:0008784 Catalysis of the reaction: L-alanine = D-alanine. 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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0042803 Binding to an identical protein to form a homodimer. 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): Y
DEG identity (%): 88.301
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 98.14

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 0.551

Structure A0A0H3GGW4

Pocket Pocket 22

P2Rank 0.907

Structure A0A0H3GGW4

Pocket Pocket 1

ColabFold model

FPocket 0.596 · Pocket 28

P2Rank 0.904 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 145 / 4744 genomes with a hit

Normalized 0.031

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)

5.1.1.1

Gene Ontology (GO)

GO:0006522 OBSOLETE. The chemical reactions and pathways involving alanine, 2-aminopropanoic acid.
GO:0008784 Catalysis of the reaction: L-alanine = D-alanine.
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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0042803 Binding to an identical protein to form a homodimer.
GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
GO:0030632 The chemical reactions and pathways resulting in the formation of D-alanine, the D-enantiomer of the amino acid alanine, i.e (2R)-2-aminopropanoic acid.

Sequence Features

Domain/signature hits from InterPro and related databases.

41 records

Show feature table

Start	End	DB	Term	Name
10	214	Gene3D	G3DSA:3.20.20.10	Alanine racemase
10	214	InterPro	IPR029066	PLP-binding barrel
3	358	Hamap	MF_01201	Alanine racemase.
3	358	InterPro	IPR000821	Alanine racemase
10	215	FunFam	G3DSA:3.20.20.10:FF:000002	Alanine racemase
234	357	Pfam	PF00842	Alanine racemase, C-terminal domain
234	357	InterPro	IPR011079	Alanine racemase, C-terminal
8	219	Pfam	PF01168	Alanine racemase, N-terminal domain
8	219	InterPro	IPR001608	Alanine racemase, N-terminal
215	359	Gene3D	G3DSA:2.40.37.10	Lyase, Ornithine Decarboxylase; Chain A, domain 1
215	359	InterPro	IPR009006	Alanine racemase/group IV decarboxylase, C-terminal
31	41	ProSitePatterns	PS00395	Alanine racemase pyridoxal-phosphate attachment site.
31	41	InterPro	IPR020622	Alanine racemase, pyridoxal-phosphate attachment site
267	282	PRINTS	PR00992	Alanine racemase signature
267	282	InterPro	IPR000821	Alanine racemase
288	305	PRINTS	PR00992	Alanine racemase signature
288	305	InterPro	IPR000821	Alanine racemase
155	166	PRINTS	PR00992	Alanine racemase signature
155	166	InterPro	IPR000821	Alanine racemase
192	219	PRINTS	PR00992	Alanine racemase signature
192	219	InterPro	IPR000821	Alanine racemase
26	42	PRINTS	PR00992	Alanine racemase signature
26	42	InterPro	IPR000821	Alanine racemase
340	353	PRINTS	PR00992	Alanine racemase signature
340	353	InterPro	IPR000821	Alanine racemase
60	78	PRINTS	PR00992	Alanine racemase signature
60	78	InterPro	IPR000821	Alanine racemase
120	132	PRINTS	PR00992	Alanine racemase signature
120	132	InterPro	IPR000821	Alanine racemase
250	265	PRINTS	PR00992	Alanine racemase signature
250	265	InterPro	IPR000821	Alanine racemase
234	358	SMART	SM01005	Ala_racemase_C_2
234	358	InterPro	IPR011079	Alanine racemase, C-terminal
3	357	CDD	cd06827	PLPDE_III_AR_proteobact
213	359	FunFam	G3DSA:2.40.37.10:FF:000002	Alanine racemase
3	358	NCBIfam	TIGR00492	alanine racemase
1	358	PANTHER	PTHR30511	ALANINE RACEMASE
8	235	SUPERFAMILY	SSF51419	PLP-binding barrel
8	235	InterPro	IPR029066	PLP-binding barrel
228	358	SUPERFAMILY	SSF50621	Alanine racemase C-terminal domain-like
228	358	InterPro	IPR009006	Alanine racemase/group IV decarboxylase, C-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_A0A0H3GGW4	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00390	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
2				0.148
1				0.129
7				0.023
6				0.004

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	31.03	0.907
2	3.12	0.084
3	1.42	0.015
4	1.4	0.015

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
28				0.596
23				0.352
30				0.31

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				19.43	0.839
2				3.13	0.106

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.

60 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
CO2	5IRP	P94494	44.0 Da LogP -0.58 TPSA 34.1	✓ Ro5	✓ Clean	`C(=O)=O`
DCS	5FAJ	O86786	333.2 Da LogP -0.78 TPSA 150.2	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H]2CONC2=O)O`
IN5	4XBJ	P0A6B4	356.2 Da LogP 0.32 TPSA 169.4	1 viol.	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](C)P(=O)(O)O)O`
L7N	6SCZ	P9WQA9	332.2 Da LogP -2.37 TPSA 152.2	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)/C=[NH+]/[C@@H]2CONC2=…`
MLI	6A2F	Q9HUN4	102.0 Da LogP -3.12 TPSA 80.3	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(=O)[O-]`
OJQ	6SCZ	P9WQA9	332.2 Da LogP -0.21 TPSA 162.8	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)C[NH2+]c2conc2O)O`
P4K	6SCZ	P9WQA9	662.8 Da LogP 0.23 TPSA 149.5	2 viol.	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
PPI	5FAG	O86786	74.1 Da LogP 0.48 TPSA 37.3	✓ Ro5	✓ Clean	`CCC(=O)O`
UAH	5IRP	P94494	219.1 Da LogP 0.70 TPSA 99.9	✓ Ro5	✓ Clean	`Cc1c(cc(cn1)COP(=O)(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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
4AX	P9WQA9	—	102.1 Da LogP -1.62 TPSA 64.3	✓ Ro5	✓ Clean	`C1[C@H](C(=O)NO1)N`

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
ZINC5650743	1.000	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC6403917	1.000	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC12501520	0.688	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC3874716	0.688	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769	0.688	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	0.688	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829	0.688	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	0.688	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5859031	0.688	294.4 Da LogP 1.13 TPSA 55.4	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCC`
ZINC1644613	0.619	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`
ZINC1580161	0.600	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	0.600	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	0.600	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654	0.600	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44076059	0.600	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	0.600	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5997860	0.600	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC2555269	0.591	220.3 Da LogP 1.22 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCOCCOCCOCCO`
ZINC4974293	0.579	280.4 Da LogP 1.08 TPSA 55.4	✓ Ro5	✓ Clean	`CCOCCOCCOCOCCOCCOCC`
ZINC100014200	0.565	494.7 Da LogP 4.02 TPSA 84.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC100070166	0.565	290.4 Da LogP 3.17 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCO`
ZINC100310628	0.565	478.7 Da LogP 4.78 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC100365196	0.565	302.5 Da LogP 4.71 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCO`
ZINC101772322	0.565	434.7 Da LogP 4.76 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC103600921	0.565	466.7 Da LogP 3.24 TPSA 84.8	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC14880431	0.565	378.6 Da LogP 3.20 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC14881140	0.565	306.4 Da LogP 2.41 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCOCCO`
ZINC16051619	0.565	350.5 Da LogP 2.42 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCOCCOCCO`
ZINC2584424	0.565	218.3 Da LogP 2.37 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCO`
ZINC4521877	0.565	234.3 Da LogP 1.61 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCOCCOCCOCCO`
ZINC5273610	0.565	322.4 Da LogP 1.64 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCOCCOCCOCCOCCOCCO`
ZINC58538366	0.565	392.6 Da LogP 3.59 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC58631420	0.565	422.6 Da LogP 3.22 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC59441819	0.565	318.5 Da LogP 3.95 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCO`
ZINC59622400	0.565	274.4 Da LogP 3.93 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCO`
ZINC71788551	0.565	334.5 Da LogP 3.19 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCO`
ZINC71788564	0.565	262.4 Da LogP 2.39 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCO`
ZINC71788567	0.565	406.6 Da LogP 3.98 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC8214594	0.565	362.6 Da LogP 3.97 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCO`
ZINC88260008	0.565	390.6 Da LogP 4.75 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCO`
ZINC95784968	0.565	450.7 Da LogP 4.00 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC95863931	0.565	464.7 Da LogP 4.39 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC1656021	0.550	233.2 Da LogP 1.01 TPSA 99.9	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(C)c1O`
ZINC1532705	0.545	249.2 Da LogP 0.20 TPSA 120.1	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(CO)c1O`
ZINC116078620	0.538	236.3 Da LogP -0.41 TPSA 74.2	✓ Ro5	✓ Clean	`CCOC(=O)COCCOCCOCCO`
ZINC83253955	0.538	206.2 Da LogP -0.03 TPSA 65.0	✓ Ro5	✓ Clean	`CCOC(=O)CCOCCOCCO`
ZINC1542984442	0.524	413.5 Da LogP -0.93 TPSA 120.1	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1857792057	0.524	474.6 Da LogP 0.06 TPSA 103.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC38917157	0.524	210.3 Da LogP -0.04 TPSA 47.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCS`
ZINC77271182	0.524	281.3 Da LogP -0.98 TPSA 92.4	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCO`

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.