Protein profile

VK055_1174

pyrF

Genome: KpATCC43816

Gene: pyrF AIK79797.1 Structure source: Experimental + ColabFold UniProt A0A0H3GNE4

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Amino acids 228

Annotations 5

Features 18

PDB binders 3

Druggability 0.65

Overview

Basic information about this protein and its source genome.

Accession: VK055_1174
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: pyrF AIK79797.1
Status: annotated
Amino acids: 228
Structure source: Experimental + ColabFold

4.1.1.23

GO:0004590 Catalysis of the reaction: H+ + orotidine 5'-phosphate = CO2 + UMP. 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:0044205 The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD+ or oxygen. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 (%): 85.526
DEG E-value: 2.71e-141
Localization: Cytoplasmic
ColabFold pLDDT: 96.04

Selected Druggability evidence

PDB experimental structure

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 0.65

Structure 8CSO

Pocket Pocket 2

P2Rank 0.688

Structure 8CSO

Pocket Pocket 1

ColabFold model

FPocket 0.529 · Pocket 4

P2Rank 0.734 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 189 / 4744 genomes with a hit

Normalized 0.04

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)

4.1.1.23

Gene Ontology (GO)

GO:0004590 Catalysis of the reaction: H+ + orotidine 5'-phosphate = CO2 + UMP.
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:0044205 The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD+ or oxygen.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records

Show feature table

Start	End	DB	Term	Name
2	220	Pfam	PF00215	Orotidine 5'-phosphate decarboxylase / HUMPS family
2	220	InterPro	IPR001754	Orotidine 5'-phosphate decarboxylase domain
1	225	Hamap	MF_01200_B	Orotidine 5'-phosphate decarboxylase [pyrF].
1	225	InterPro	IPR047596	Orotidine 5'-phosphate decarboxylase, bacterial
1	228	FunFam	G3DSA:3.20.20.70:FF:000015	Orotidine 5'-phosphate decarboxylase
1	223	SUPERFAMILY	SSF51366	Ribulose-phoshate binding barrel
1	223	InterPro	IPR011060	Ribulose-phosphate binding barrel
1	220	CDD	cd04725	OMP_decarboxylase_like
1	220	SMART	SM00934	OMPdecase_2
1	220	InterPro	IPR001754	Orotidine 5'-phosphate decarboxylase domain
2	223	PANTHER	PTHR32119	OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
2	223	InterPro	IPR014732	Orotidine 5'-phosphate decarboxylase
51	64	ProSitePatterns	PS00156	Orotidine 5'-phosphate decarboxylase active site.
51	64	InterPro	IPR018089	Orotidine 5'-phosphate decarboxylase, active site
1	228	Gene3D	G3DSA:3.20.20.70	Aldolase class I
1	228	InterPro	IPR013785	Aldolase-type TIM barrel
2	220	NCBIfam	TIGR01740	orotidine-5'-phosphate decarboxylase
2	220	InterPro	IPR014732	Orotidine 5'-phosphate decarboxylase

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

1 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
PDB 8CSO	X-ray	2.60 Å	A,B,C,D,E,F,G,H,I,J	99.6% 2-228	PDBe RCSB PDBj File	Viewing
ColabFold VK055_1174	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
12				0.802
16				0.297
134				0.226
116				0.222

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	18.3	0.82
2	16.9	0.79
3	15.81	0.763
4	15.59	0.757
5	14.48	0.724

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
4				0.529
1				0.343

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	9.51	0.511
2	3.64	0.137
3	1.59	0.025
4	0.9	0.004

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.

53 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
BMP	1JJK	P08244	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)…`
BMQ	1EIX	P08244	340.2 Da LogP -2.99 TPSA 182.9	✓ Ro5	✓ Clean	`C1C(=O)NC(=O)N(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O…`
XPE	3UWQ	Q9KQT7	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`C(COCCOCCOCCOCCOCCOCCOCCOCCOCCO)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
ZINC12501520	1.000	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC3870485	1.000	340.2 Da LogP -2.99 TPSA 182.9	✓ Ro5	✓ Clean	`O=C1CC(=O)N([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3870486	1.000	340.2 Da LogP -2.99 TPSA 182.9	✓ Ro5	✓ Clean	`O=C1CC(=O)N([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O…`
ZINC3870487	1.000	340.2 Da LogP -2.99 TPSA 182.9	✓ Ro5	✓ Clean	`O=C1CC(=O)N([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3870488	1.000	340.2 Da LogP -2.99 TPSA 182.9	✓ Ro5	✓ Clean	`O=C1CC(=O)N([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O…`
ZINC3874716	1.000	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769	1.000	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	1.000	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829	1.000	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	1.000	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
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)(…`
ZINC115086873	0.688	209.2 Da LogP -1.08 TPSA 83.2	✓ Ro5	✓ Clean	`NOCCOCCOCCOCCO`
ZINC137432264	0.688	457.6 Da LogP -0.91 TPSA 129.3	1 viol.	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC146143823	0.688	237.3 Da LogP -1.00 TPSA 83.2	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCO`
ZINC1542984442	0.688	413.5 Da LogP -0.93 TPSA 120.1	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1565503710	0.688	254.3 Da LogP -0.03 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCS`
ZINC1580161	0.688	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	0.688	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	0.688	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1857792028	0.688	430.6 Da LogP 0.04 TPSA 94.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC1857792057	0.688	474.6 Da LogP 0.06 TPSA 103.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC230494776	0.688	325.4 Da LogP -0.96 TPSA 101.6	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654	0.688	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC38917157	0.688	210.3 Da LogP -0.04 TPSA 47.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCS`
ZINC44076059	0.688	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	0.688	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5650743	0.688	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC5997860	0.688	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC6403917	0.688	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC77271182	0.688	281.3 Da LogP -0.98 TPSA 92.4	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCO`
ZINC83253921	0.688	369.5 Da LogP -0.95 TPSA 110.9	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC90741446	0.688	386.5 Da LogP 0.02 TPSA 84.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC90741447	0.688	298.4 Da LogP -0.01 TPSA 66.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCS`
ZINC5439332	0.667	260.2 Da LogP -3.11 TPSA 136.4	✓ Ro5	✓ Clean	`O=C1CC(=O)N([C@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)C…`
ZINC5439333	0.667	260.2 Da LogP -3.11 TPSA 136.4	✓ Ro5	✓ Clean	`O=C1CC(=O)N([C@@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)…`
ZINC5439335	0.667	260.2 Da LogP -3.11 TPSA 136.4	✓ Ro5	✓ Clean	`O=C1CC(=O)N([C@H]2O[C@@H](CO)[C@@H](O)[C@@H]2O)…`
ZINC5439336	0.667	260.2 Da LogP -3.11 TPSA 136.4	✓ Ro5	✓ Clean	`O=C1CC(=O)N([C@@H]2O[C@@H](CO)[C@@H](O)[C@@H]2O…`
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@…`
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…`

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.