Protein profile

KP13_04669

D-amino acid dehydrogenase 2 small subunit

Genome: KpKP13

Gene: dadA2 AHE44071.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GRA8

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Amino acids 417

Annotations 5

Features 17

PDB binders 6

Druggability 0.794

Overview

Basic information about this protein and its source genome.

Accession: KP13_04669
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: dadA2 AHE44071.1
Status: annotated
Amino acids: 417
Structure source: AlphaFold + ColabFold

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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0008718 Catalysis of the reaction: a D-alpha-amino acid + a quinone + H2O = a 2-oxocarboxylate + a quinol + NH4+. GO:0055130 The chemical reactions and pathways resulting in the breakdown of D-alanine.

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: CytoplasmicMembrane
ColabFold pLDDT: 95.43

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 0.794

Structure A0A0H3GRA8

Pocket Pocket 14

P2Rank 0.988

Structure A0A0H3GRA8

Pocket Pocket 1

ColabFold model

FPocket 0.927 · Pocket 25

P2Rank 0.989 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 17 / 4744 genomes with a hit

Normalized 0.004

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0008718 Catalysis of the reaction: a D-alpha-amino acid + a quinone + H2O = a 2-oxocarboxylate + a quinol + NH4+.
GO:0055130 The chemical reactions and pathways resulting in the breakdown of D-alanine.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records

Show feature table

Start	End	DB	Term	Name
5	22	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
3	415	SUPERFAMILY	SSF51905	FAD/NAD(P)-binding domain
3	415	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
1	18	Phobius	SIGNAL_PEPTIDE	Signal peptide region
5	13	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
14	18	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
2	69	Gene3D	G3DSA:3.50.50.60	-
2	69	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
271	360	SUPERFAMILY	SSF54373	FAD-linked reductases, C-terminal domain
3	400	PANTHER	PTHR13847	SARCOSINE DEHYDROGENASE-RELATED
19	417	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
137	359	Gene3D	G3DSA:3.30.9.10	-
103	399	Gene3D	G3DSA:3.50.50.60	-
103	399	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
1	4	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
4	394	Pfam	PF01266	FAD dependent oxidoreductase
4	394	InterPro	IPR006076	FAD dependent oxidoreductase

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_A0A0H3GRA8	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_04669	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
14				0.794
4				0.747
2				0.517

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	35.29	0.953
2	5.14	0.237
3	5.08	0.232
4	3.07	0.102
5	2.09	0.047

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
25				0.927
2				0.339

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	20.82	0.862
2	15.53	0.755
3	5.97	0.293
4	3.88	0.152
5	1.78	0.033

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
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…`
MTG	3AD7	Q50LF2	105.1 Da LogP -0.90 TPSA 40.1	✓ Ro5	✓ Clean	`CSCC(=O)[O-]`
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`
ZINC16051927	0.563	216.3 Da LogP 2.96 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCC[C@@H](O)CC(=O)O`
ZINC2558055	0.563	202.3 Da LogP 2.57 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCC[C@H](O)CC(=O)O`
ZINC59297041	0.563	200.3 Da LogP 3.85 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCC[C@@H](C)CC(=O)O`
ZINC85915165	0.563	202.3 Da LogP 2.57 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCC[C@@H](O)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.