Protein profile

VK055_0143

FAD dependent oxidoreductase family protein

Genome: KpATCC43816

Gene: AIK78771.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GRR7

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Amino acids 423

Annotations 3

Features 14

PDB binders 9

Druggability 0.934

Overview

Basic information about this protein and its source genome.

Accession: VK055_0143
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK78771.1
Status: annotated
Amino acids: 423
Structure source: AlphaFold + ColabFold

GO:0019478 The chemical reactions and pathways resulting in the breakdown of D-amino acids, the D-enantiomers of amino acids. GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. GO:0008718 Catalysis of the reaction: a D-alpha-amino acid + a quinone + H2O = a 2-oxocarboxylate + a quinol + NH4+.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 23.148
Human E-value: 7.43e-08
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 88.889
DEG E-value: 0.0
Localization: CytoplasmicMembrane
ColabFold pLDDT: 93.02

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 0.934

Structure A0A0H3GRR7

Pocket Pocket 2

P2Rank 0.988

Structure A0A0H3GRR7

Pocket Pocket 1

ColabFold model

FPocket 0.453 · Pocket 19

P2Rank 0.993 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 157 / 4744 genomes with a hit

Normalized 0.033

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

GO:0019478 The chemical reactions and pathways resulting in the breakdown of D-amino acids, the D-enantiomers of amino acids.
GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
GO:0008718 Catalysis of the reaction: a D-alpha-amino acid + a quinone + H2O = a 2-oxocarboxylate + a quinol + NH4+.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records

Show feature table

Start	End	DB	Term	Name
1	401	Hamap	MF_01202	D-amino acid dehydrogenase [dadA].
1	401	InterPro	IPR023080	D-amino acid dehydrogenase DadA
2	53	Gene3D	G3DSA:3.50.50.60	-
2	53	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
260	350	SUPERFAMILY	SSF54373	FAD-linked reductases, C-terminal domain
125	353	Gene3D	G3DSA:3.30.9.10	-
2	410	SUPERFAMILY	SSF51905	FAD/NAD(P)-binding domain
2	410	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
96	394	Gene3D	G3DSA:3.50.50.60	-
96	394	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
2	405	PANTHER	PTHR13847	SARCOSINE DEHYDROGENASE-RELATED
1	388	Pfam	PF01266	FAD dependent oxidoreductase
1	388	InterPro	IPR006076	FAD dependent oxidoreductase
1	53	FunFam	G3DSA:3.50.50.60:FF:000020	D-amino acid dehydrogenase

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_A0A0H3GRR7	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_0143	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				0.934
14				0.23

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	25.39	0.906
2	15.89	0.765
3	8.26	0.44
4	3.8	0.147
5	3.27	0.114

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				0.453
24				0.401
1				0.238

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	56.13	0.984
2	3.46	0.126
3	3.43	0.124
4	1.56	0.024

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.

59 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
AAC	1NG3	O31616	117.1 Da LogP -0.79 TPSA 66.4	✓ Ro5	✓ Clean	`CC(=O)NCC(=O)O`
B6X	6J39	X5IYZ1	248.3 Da LogP 2.62 TPSA 74.6	✓ Ro5	✓ Clean	`CCCCCC[C@H](CC(=O)O)SCC(=O)O`
DMG	1VRQ	Q50LF2	103.1 Da LogP -0.37 TPSA 40.5	✓ Ro5	✓ Clean	`CN(C)CC(=O)O`
FOA	2GAG	Q3ZDR0	112.1 Da LogP 0.98 TPSA 50.4	✓ Ro5	✓ Clean	`c1cc(oc1)C(=O)O`
FON	1VRQ	Q50LF2	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC[C@@H]2…`
GOA	1RYI	O31616	76.1 Da LogP -0.94 TPSA 57.5	✓ Ro5	✓ Clean	`C(C(=O)O)O`
MTG	3AD7	Q50LF2	105.1 Da LogP -0.90 TPSA 40.1	✓ Ro5	✓ Clean	`CSCC(=O)[O-]`
PEO	1NG4	O31616	34.0 Da LogP 0.02 TPSA 40.5	✓ Ro5	✓ Clean	`OO`
PYC	3AD8	Q50LF2	110.1 Da LogP -0.62 TPSA 55.9	✓ Ro5	✓ Clean	`c1cc([nH]c1)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).

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
ZINC9212425	0.803	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CNc1ccc(C(=O)N[…`
ZINC9212426	0.803	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@H](CNc1ccc(C(=O)N[C…`
ZINC9212427	0.803	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CNc1ccc(C(=O)N[…`
ZINC9212428	0.803	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@H](CNc1ccc(C(=O)N[C…`
ZINC200768381	0.727	344.3 Da LogP -0.08 TPSA 153.4	✓ Ro5	✓ Clean	`Nc1nc(=O)c2c([nH]1)NC[C@@H](CNc1ccc(C(=O)O)cc1)…`
ZINC200768411	0.727	344.3 Da LogP -0.08 TPSA 153.4	✓ Ro5	✓ Clean	`Nc1nc(=O)c2c([nH]1)NC[C@H](CNc1ccc(C(=O)O)cc1)N…`
ZINC8628600	0.716	473.5 Da LogP 0.13 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c([nH]c(N)nc2=O)NC[C@@H]1CCNc1ccc(C(=O)N[C…`
ZINC8628601	0.716	473.5 Da LogP 0.13 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c([nH]c(N)nc2=O)NC[C@H]1CCNc1ccc(C(=O)N[C@…`
ZINC8655682	0.688	487.5 Da LogP -0.34 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CCNc1ccc(C(=O)N…`
ZINC85394426	0.667	206.2 Da LogP 1.80 TPSA 80.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccco2)o1`
ZINC8997303	0.667	487.5 Da LogP 0.07 TPSA 220.1	1 viol.	✓ Clean	`Nc1nc(O)c2c(n1)NC[C@@H](CNc1ccc(C(=O)N[C@@H](CC…`
ZINC8997304	0.667	487.5 Da LogP 0.07 TPSA 220.1	1 viol.	✓ Clean	`Nc1nc(O)c2c(n1)NC[C@@H](CNc1ccc(C(=O)N[C@H](CCC…`
ZINC8997305	0.667	487.5 Da LogP 0.07 TPSA 220.1	1 viol.	✓ Clean	`Nc1nc(O)c2c(n1)NC[C@H](CNc1ccc(C(=O)N[C@@H](CCC…`
ZINC8997306	0.667	487.5 Da LogP 0.07 TPSA 220.1	1 viol.	✓ Clean	`Nc1nc(O)c2c(n1)NC[C@H](CNc1ccc(C(=O)N[C@H](CCCC…`
ZINC2005305	0.658	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@@H]1CNc1ccc(C(=O)N[C@…`
ZINC2572666	0.658	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@H]1CNc1ccc(C(=O)N[C@@…`
ZINC4228266	0.658	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@@H]1CNc1ccc(C(=O)N[C@…`
ZINC4228267	0.658	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@H]1CNc1ccc(C(=O)N[C@H…`
ZINC2377216	0.633	216.3 Da LogP 2.52 TPSA 74.6	✓ Ro5	✓ Clean	`CCCCCCC(CC(=O)O)CC(=O)O`
ZINC12374887	0.630	216.2 Da LogP 2.21 TPSA 67.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccco2)cc1`
ZINC169748282	0.623	471.4 Da LogP -0.26 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc(=O)c2c([nH]1)NC=C(CNc1ccc(C(=O)N[C@@H](CC…`
ZINC1710770	0.615	200.2 Da LogP 2.35 TPSA 47.3	✓ Ro5	Alert	`O=C(C(=O)c1ccco1)c1ccccc1`
ZINC8655681	0.613	487.5 Da LogP 0.07 TPSA 220.1	1 viol.	✓ Clean	`Nc1nc(O)c2c(n1)NC[C@@H](CCNc1ccc(C(=O)N[C@@H](C…`
ZINC8655685	0.613	487.5 Da LogP 0.07 TPSA 220.1	1 viol.	✓ Clean	`Nc1nc(O)c2c(n1)NC[C@H](CCNc1ccc(C(=O)N[C@H](CCC…`
ZINC8667682	0.613	487.5 Da LogP 0.07 TPSA 220.1	1 viol.	✓ Clean	`Nc1nc(O)c2c(n1)NC[C@@H](CCNc1ccc(C(=O)N[C@H](CC…`
ZINC223670610	0.610	459.5 Da LogP -0.28 TPSA 194.0	1 viol.	✓ Clean	`CN(c1ccc(C(=O)N[C@@H](CCC(=O)O)C(=O)O)cc1)[C@@H…`
ZINC3870062	0.610	457.4 Da LogP -0.52 TPSA 194.0	1 viol.	✓ Clean	`Nc1nc(=O)c2c([nH]1)NC[C@H]1CN(c3ccc(C(=O)N[C@H]…`
ZINC1613560	0.607	216.2 Da LogP 2.21 TPSA 67.5	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)c1ccco1`
ZINC100477623	0.600	204.2 Da LogP 2.33 TPSA 60.4	✓ Ro5	✓ Clean	`O=C(CC(=O)c1ccco1)c1ccco1`
ZINC1637602	0.600	443.5 Da LogP 0.62 TPSA 187.5	1 viol.	✓ Clean	`Nc1nc(=O)c2c([nH]1)NC[C@@H](CCc1ccc(C(=O)N[C@@H…`
ZINC2392141	0.600	214.3 Da LogP 4.24 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCC(CCCCC)CC(=O)O`
ZINC6472822	0.600	218.2 Da LogP 2.72 TPSA 60.4	✓ Ro5	✓ Clean	`O=C(CCC(=O)c1ccco1)c1ccco1`
ZINC4228235	0.597	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@H](CNc1ccc(C(=O)N[C@@H](…`
ZINC4228236	0.597	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@H](CNc1ccc(C(=O)N[C@H](C…`
ZINC4228237	0.597	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@@H](CNc1ccc(C(=O)N[C@@H]…`
ZINC4228238	0.597	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@@H](CNc1ccc(C(=O)N[C@H](…`
ZINC2578862	0.594	200.3 Da LogP 3.85 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCC[C@H](CC)CC(=O)O`
ZINC59199046	0.594	200.3 Da LogP 3.85 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCC[C@@H](CC)CC(=O)O`
ZINC156403	0.593	274.3 Da LogP 1.47 TPSA 66.9	✓ Ro5	✓ Clean	`O=C(c1ccco1)N1CCN(C(=O)c2ccco2)CC1`
ZINC8536462	0.587	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc(=O)c2c([nH]1)NC[C@H](CN(C=O)c1ccc(C(=O)N[…`
ZINC19367002	0.579	204.2 Da LogP -0.98 TPSA 81.1	✓ Ro5	✓ Clean	`CN(CCN(C)CC(=O)O)CC(=O)O`
ZINC12496906	0.577	457.4 Da LogP 0.22 TPSA 202.8	1 viol.	✓ Clean	`CN1C(CNc2ccc(C(=O)N[C@@H](CCC(=O)O)C(=O)O)cc2)=…`
ZINC983943	0.577	360.3 Da LogP 4.16 TPSA 90.6	✓ Ro5	✓ Clean	`O=C(c1cc(C(=O)c2ccco2)cc(C(=O)c2ccco2)c1)c1ccco1`
ZINC106891773	0.571	204.2 Da LogP 2.65 TPSA 63.6	✓ Ro5	✓ Clean	`O=C(/C=C(\O)c1ccco1)c1ccco1`
ZINC19364891	0.571	204.2 Da LogP -0.98 TPSA 81.1	✓ Ro5	✓ Clean	`CN(C)CCN(CC(=O)O)CC(=O)O`
ZINC49815930	0.567	216.2 Da LogP 2.21 TPSA 67.5	✓ Ro5	✓ Clean	`O=C(O)c1cccc(C(=O)c2ccco2)c1`
ZINC100305273	0.563	286.5 Da LogP 4.91 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC[C@H](O)CC(=O)O`
ZINC100305277	0.563	286.5 Da LogP 4.91 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC[C@@H](O)CC(=O)O`
ZINC32838984	0.563	272.4 Da LogP 4.52 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC[C@@H](O)CC(=O)O`
ZINC59658579	0.563	214.3 Da LogP 4.24 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCC[C@@H](C)CC(=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.