Protein profile

KP13_01217

3-keto-L-gulonate-6-phosphate decarboxylase ulaD

Genome: KpKP13

Gene: ulaD AHE46717.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GQN9

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Amino acids 216

Annotations 5

Features 17

PDB binders 8

Druggability 0.656

Overview

Basic information about this protein and its source genome.

Accession: KP13_01217
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: ulaD AHE46717.1
Status: annotated
Amino acids: 216
Structure source: AlphaFold + ColabFold

4.1.1.85

GO:0006207 The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors. GO:0004590 Catalysis of the reaction: H+ + orotidine 5'-phosphate = CO2 + UMP. GO:0033982 Catalysis of the reaction: 3-dehydro-L-gulonate 6-phosphate + H+ = L-xylulose 5-phosphate + CO2. GO:0019854 The chemical reactions and pathways resulting in the breakdown of L-ascorbic acid; L-ascorbic acid ionizes to give L-ascorbate, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate, which is required as a cofactor in the oxidation of prolyl residues to hydroxyprolyl, and other reactions.

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: Cytoplasmic
ColabFold pLDDT: 98.03

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 0.656

Structure A0A0H3GQN9

Pocket Pocket 5

P2Rank 0.889

Structure A0A0H3GQN9

Pocket Pocket 1

ColabFold model

FPocket 0.388 · Pocket 10

P2Rank 0.882 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 70 / 4744 genomes with a hit

Normalized 0.015

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

4.1.1.85

Gene Ontology (GO)

GO:0006207 The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
GO:0004590 Catalysis of the reaction: H+ + orotidine 5'-phosphate = CO2 + UMP.
GO:0033982 Catalysis of the reaction: 3-dehydro-L-gulonate 6-phosphate + H+ = L-xylulose 5-phosphate + CO2.
GO:0019854 The chemical reactions and pathways resulting in the breakdown of L-ascorbic acid; L-ascorbic acid ionizes to give L-ascorbate, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate, which is required as a cofactor in the oxidation of prolyl residues to hydroxyprolyl, and other reactions.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records

Show feature table

Start	End	DB	Term	Name
19	216	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
11	18	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
3	213	PANTHER	PTHR35039	3-KETO-L-GULONATE-6-PHOSPHATE DECARBOXYLASE SGBH-RELATED
1	2	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
3	10	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
4	207	CDD	cd04726	KGPDC_HPS
4	207	InterPro	IPR041710	HPS/KGPDC domain
1	18	Phobius	SIGNAL_PEPTIDE	Signal peptide region
3	213	FunFam	G3DSA:3.20.20.70:FF:000022	3-keto-L-gulonate-6-phosphate decarboxylase UlaD
5	214	Gene3D	G3DSA:3.20.20.70	Aldolase class I
5	214	InterPro	IPR013785	Aldolase-type TIM barrel
5	207	SMART	SM00934	OMPdecase_2
5	207	InterPro	IPR001754	Orotidine 5'-phosphate decarboxylase domain
2	215	SUPERFAMILY	SSF51366	Ribulose-phoshate binding barrel
2	215	InterPro	IPR011060	Ribulose-phosphate binding barrel
5	206	Pfam	PF00215	Orotidine 5'-phosphate decarboxylase / HUMPS family
5	206	InterPro	IPR001754	Orotidine 5'-phosphate decarboxylase domain

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_A0A0H3GQN9	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_01217	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				0.656
9				0.301
6				0.207

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	19.74	0.844
2	4.09	0.164
3	3.31	0.117

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
10				0.388
3				0.201

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	18.32	0.82
2	2.71	0.081
3	2.4	0.064

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.

58 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
5RP	1XBV	P39304	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`C([C@H]([C@H](C(=O)CO)O)O)OP(=O)(O)O`
BMP	4MUZ	O29333	340.2 Da LogP -3.03 TPSA 191.5	1 viol.	✓ Clean	`C1=C(N(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)…`
HMS	1XBX	P39304	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`C([C@@H]([C@@H](C(=O)CO)O)O)OP(=O)(O)O`
LG6	1KW1	P39304	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`C([C@@H]([C@H]([C@@H]([C@@H](C(=O)O)O)O)O)O)OP(…`
LX1	1Q6R	P39304	216.1 Da LogP -1.80 TPSA 127.5	✓ Ro5	✓ Clean	`C[C@H]([C@@H]([C@H](COP(=O)(O)O)O)O)O`
LXP	1Q6Q	P39304	232.1 Da LogP -2.83 TPSA 147.7	1 viol.	✓ Clean	`C([C@H]([C@@H]([C@H](COP(=O)(O)O)O)O)O)O`
MLI	3F4W	Q8ZMP9	102.0 Da LogP -3.12 TPSA 80.3	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(=O)[O-]`
TX4	1Q6L	P39304	233.1 Da LogP -2.89 TPSA 159.7	1 viol.	✓ Clean	`C([C@@H]([C@H](C(NO)O)O)O)OP(=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
ZINC12501558	1.000	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@@H](O)COP(=O)(…`
ZINC12501560	1.000	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O…`
ZINC12501562	1.000	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)…`
ZINC12501564	1.000	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@H](O)COP(=O)(…`
ZINC1529626	1.000	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC1532567	1.000	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC1532623	1.000	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(…`
ZINC1532851	1.000	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC2047359	1.000	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)COP(=O…`
ZINC2545091	1.000	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O…`
ZINC30320708	1.000	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC3869602	1.000	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)COP(=…`
ZINC3869603	1.000	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)COP(=O…`
ZINC3869604	1.000	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)…`
ZINC2516111	0.917	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)CO`
ZINC2522704	0.917	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO`
ZINC3869812	0.917	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC100065511	0.793	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC100085043	0.793	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC104869937	0.793	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC13537943	0.793	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC85994845	0.793	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC5132038	0.767	290.2 Da LogP -3.90 TPSA 185.0	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)COP(=O)…`
ZINC5975509	0.760	202.1 Da LogP -2.19 TPSA 127.5	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H](O)[C@H](O)CO`
ZINC100351015	0.745	368.2 Da LogP -3.04 TPSA 208.6	1 viol.	✓ Clean	`O=C(O)c1cc(=O)[nH]c(=O)n1[C@@H]1O[C@H](COP(=O)(…`
ZINC4095542	0.745	368.2 Da LogP -3.04 TPSA 208.6	1 viol.	✓ Clean	`O=C(O)c1cc(=O)[nH]c(=O)n1[C@@H]1O[C@H](COP(=O)(…`
ZINC3870277	0.724	310.1 Da LogP -2.50 TPSA 191.0	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC12503831	0.647	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@H]2…`
ZINC12503833	0.647	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@@H]…`
ZINC13512000	0.647	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@H]…`
ZINC1532538	0.647	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@@H…`
ZINC2026984	0.647	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@H]…`
ZINC2123545	0.647	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)[C@H…`
ZINC2606131	0.647	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)[C@@…`
ZINC36377965	0.647	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@@H…`
ZINC3870257	0.647	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@H…`
ZINC3870258	0.647	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@…`
ZINC3870259	0.647	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@@…`
ZINC3870260	0.647	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@…`
ZINC9235501	0.647	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@H…`
ZINC25721582	0.633	244.1 Da LogP -2.23 TPSA 144.5	✓ Ro5	✓ Clean	`O=CC[C@H](O)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC25721586	0.633	244.1 Da LogP -2.23 TPSA 144.5	✓ Ro5	✓ Clean	`O=CC[C@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC4544030	0.633	244.1 Da LogP -2.23 TPSA 144.5	✓ Ro5	✓ Clean	`O=CC[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4544032	0.633	244.1 Da LogP -2.23 TPSA 144.5	✓ Ro5	✓ Clean	`O=CC[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4544034	0.633	244.1 Da LogP -2.23 TPSA 144.5	✓ Ro5	✓ Clean	`O=CC[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC4887586	0.633	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4887587	0.633	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4887588	0.633	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC4887589	0.633	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC4705962	0.623	325.2 Da LogP -3.34 TPSA 184.2	✓ Ro5	✓ Clean	`O=c1cnn([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@…`

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.