Protein profile

VK055_1392

dihydroorotase, homodimeric type

Genome: KpATCC43816

Gene: pyrC AIK80015.1 Structure source: AlphaFold + ColabFold UniProt A6T7D6

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Amino acids 341

Annotations 4

Features 17

PDB binders 10

Druggability 0.304

Overview

Basic information about this protein and its source genome.

Accession: VK055_1392
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: pyrC AIK80015.1
Status: annotated
Amino acids: 341
Structure source: AlphaFold + ColabFold

GO:0019856 The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases. GO:0016812 Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a cyclic amide. GO:0004151 Catalysis of the reaction: (S)-dihydroorotate + H2O = N-carbamoyl-L-aspartate + H+. GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.

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 (%): 86.51
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 97.94

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 0.304

Structure A6T7D6

Pocket Pocket 1

P2Rank 0.414

Structure A6T7D6

Pocket Pocket 1

ColabFold model

FPocket 0.657 · Pocket 9

P2Rank 0.3 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 155 / 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.

4 GO

Gene Ontology (GO)

GO:0019856 The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
GO:0016812 Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a cyclic amide.
GO:0004151 Catalysis of the reaction: (S)-dihydroorotate + H2O = N-carbamoyl-L-aspartate + H+.
GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records

Show feature table

Start	End	DB	Term	Name
1	341	FunFam	G3DSA:3.20.20.140:FF:000006	Dihydroorotase
1	340	NCBIfam	TIGR00856	dihydroorotase, homodimeric type
1	340	InterPro	IPR004721	Dihydroorotase homodimeric type
1	337	CDD	cd01294	DHOase
1	337	InterPro	IPR004721	Dihydroorotase homodimeric type
1	340	Hamap	MF_00219	Dihydroorotase [pyrC].
2	339	SUPERFAMILY	SSF51556	Metallo-dependent hydrolases
2	339	InterPro	IPR032466	Metal-dependent hydrolase
2	340	PANTHER	PTHR43137	DIHYDROOROTASE
2	340	InterPro	IPR004721	Dihydroorotase homodimeric type
1	341	Gene3D	G3DSA:3.20.20.140	-
1	341	PIRSF	PIRSF001237	Dihydroorotase
1	341	InterPro	IPR004721	Dihydroorotase homodimeric type
242	253	ProSitePatterns	PS00483	Dihydroorotase signature 2.
242	253	InterPro	IPR002195	Dihydroorotase, conserved site
8	300	Pfam	PF01979	Amidohydrolase family
8	300	InterPro	IPR006680	Amidohydrolase-related

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_A6T7D6	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_1392	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
1				0.304
12				0.277
7				0.052
5				0.001

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	9.01	0.414
2	3.47	0.1
3	2.35	0.05
4	2.21	0.044
5	1.79	0.028

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
9				0.657
17				0.508
3				0.151
2				0.016

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	6.94	0.3
2	3.71	0.114
3	3.27	0.091
4	2.49	0.056
5	1.81	0.028

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
CP	3MJM	B1IV40	141.0 Da LogP -0.83 TPSA 109.9	✓ Ro5	✓ Clean	`C(=O)(N)OP(=O)(O)O`
DOR	3MJM	B1IV40	158.1 Da LogP -1.33 TPSA 95.5	✓ Ro5	✓ Clean	`C1[C@H](NC(=O)NC1=O)C(=O)O`
FLC	3D6N	O66990	189.1 Da LogP -5.25 TPSA 140.6	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O`
FOT	2E25	P05020	174.1 Da LogP -1.10 TPSA 103.0	✓ Ro5	✓ Clean	`C1(=C(NC(=O)NC1=O)C(=O)O)F`
MLI	2Z26	P05020	102.0 Da LogP -3.12 TPSA 80.3	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(=O)[O-]`
MLT	6CTY	Q8ZFU4	134.1 Da LogP -1.09 TPSA 94.8	✓ Ro5	✓ Clean	`C([C@H](C(=O)O)O)C(=O)O`
NCD	3MJM	B1IV40	176.1 Da LogP -1.42 TPSA 129.7	✓ Ro5	✓ Clean	`C([C@@H](C(=O)O)NC(=O)N)C(=O)O`
ORO	1J79	P05020	156.1 Da LogP -1.24 TPSA 103.0	✓ Ro5	✓ Clean	`C1=C(NC(=O)NC1=O)C(=O)O`
OTD	2EG7	P05020	186.1 Da LogP -1.28 TPSA 115.7	✓ Ro5	✓ Clean	`C1=C(NC(=O)N[C@H]1C(=O)O)C(=O)O`
PAL	4BJH	O66990	255.1 Da LogP -1.79 TPSA 161.2	✓ Ro5	✓ Clean	`C([C@@H](C(=O)O)NC(=O)CP(=O)(O)O)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
ZINC5131744	0.609	249.2 Da LogP -1.57 TPSA 161.2	✓ Ro5	✓ Clean	`O=C(O)C[C@H](N[C@@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC5131745	0.609	249.2 Da LogP -1.57 TPSA 161.2	✓ Ro5	✓ Clean	`O=C(O)C[C@H](N[C@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC5131908	0.609	249.2 Da LogP -1.57 TPSA 161.2	✓ Ro5	✓ Clean	`O=C(O)C[C@@H](N[C@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC1575288	0.593	248.2 Da LogP -2.17 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@@H](CC(=O)O)C(=O)N[C@@H](CC(=O)O)C(=O)O`
ZINC1575289	0.593	248.2 Da LogP -2.17 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@H](CC(=O)O)C(=O)N[C@@H](CC(=O)O)C(=O)O`
ZINC1575290	0.593	248.2 Da LogP -2.17 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@@H](CC(=O)O)C(=O)N[C@H](CC(=O)O)C(=O)O`
ZINC1575291	0.593	248.2 Da LogP -2.17 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@H](CC(=O)O)C(=O)N[C@H](CC(=O)O)C(=O)O`
ZINC1642634	0.593	200.1 Da LogP -1.54 TPSA 140.3	✓ Ro5	✓ Clean	`O=C(O)c1[nH]c(=O)[nH]c(=O)c1C(=O)O`
ZINC1642475	0.571	282.0 Da LogP -0.63 TPSA 103.0	✓ Ro5	✓ Clean	`O=C(O)c1[nH]c(=O)[nH]c(=O)c1I`
ZINC1666478	0.571	235.0 Da LogP -0.48 TPSA 103.0	✓ Ro5	✓ Clean	`O=C(O)c1[nH]c(=O)[nH]c(=O)c1Br`
ZINC1709621	0.571	248.2 Da LogP -2.17 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@@H](CC(=O)N[C@@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC1709622	0.571	248.2 Da LogP -2.17 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@H](CC(=O)N[C@@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC1709623	0.571	248.2 Da LogP -2.17 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@@H](CC(=O)N[C@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC1709624	0.571	248.2 Da LogP -2.17 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@H](CC(=O)N[C@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC1731782	0.571	204.2 Da LogP -1.62 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@H](N)C(=O)N[C@@H](CC(=O)O)C(=O)O`
ZINC1731783	0.571	204.2 Da LogP -1.62 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@@H](N)C(=O)N[C@@H](CC(=O)O)C(=O)O`
ZINC1731784	0.571	204.2 Da LogP -1.62 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@H](N)C(=O)N[C@H](CC(=O)O)C(=O)O`
ZINC1731785	0.571	204.2 Da LogP -1.62 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@@H](N)C(=O)N[C@H](CC(=O)O)C(=O)O`
ZINC969509	0.563	213.1 Da LogP -2.12 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CNC(=O)c1cc(=O)[nH]c(=O)[nH]1`
ZINC22040791	0.560	292.2 Da LogP -1.98 TPSA 173.3	1 viol.	✓ Clean	`O=C(O)C[C@H](NCCN[C@@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC22589819	0.560	292.2 Da LogP -1.98 TPSA 173.3	1 viol.	✓ Clean	`O=C(O)C[C@@H](NCCN[C@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC23377883	0.560	292.2 Da LogP -1.98 TPSA 173.3	1 viol.	✓ Clean	`O=C(O)C[C@H](NCCN[C@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC100655912	0.552	478.4 Da LogP -4.25 TPSA 299.8	1 viol.	✓ Clean	`N[C@H](CC(=O)O)C(=O)N[C@H](CC(=O)O)C(=O)N[C@H](…`
ZINC100655916	0.552	478.4 Da LogP -4.25 TPSA 299.8	1 viol.	✓ Clean	`N[C@H](CC(=O)O)C(=O)N[C@H](CC(=O)O)C(=O)N[C@@H]…`
ZINC2522588	0.552	220.2 Da LogP -2.65 TPSA 149.9	✓ Ro5	✓ Clean	`N[C@@H](CO)C(=O)N[C@@H](CC(=O)O)C(=O)O`
ZINC255993703	0.552	478.4 Da LogP -4.25 TPSA 299.8	1 viol.	✓ Clean	`N[C@H](CC(=O)O)C(=O)N[C@H](CC(=O)O)C(=O)N[C@H](…`
ZINC4533843	0.552	363.3 Da LogP -3.21 TPSA 233.4	1 viol.	✓ Clean	`N[C@@H](CC(=O)O)C(=O)N[C@@H](CC(=O)O)C(=O)N[C@@…`
ZINC4533848	0.552	478.4 Da LogP -4.25 TPSA 299.8	1 viol.	✓ Clean	`N[C@@H](CC(=O)O)C(=O)N[C@@H](CC(=O)O)C(=O)N[C@@…`
ZINC4533853	0.552	478.4 Da LogP -4.25 TPSA 299.8	1 viol.	✓ Clean	`N[C@H](CC(=O)O)C(=O)N[C@H](CC(=O)O)C(=O)N[C@@H]…`
ZINC205410870	0.545	202.1 Da LogP -0.62 TPSA 92.0	✓ Ro5	✓ Clean	`CCOC(=O)c1[nH]c(=O)[nH]c(=O)c1F`
ZINC8268096	0.545	231.2 Da LogP 0.32 TPSA 94.8	✓ Ro5	✓ Clean	`O=C(Nc1ccccc1)c1cc(=O)[nH]c(=O)[nH]1`
ZINC3311136	0.543	218.2 Da LogP 1.01 TPSA 78.4	✓ Ro5	✓ Clean	`O=C1NC(C(=O)O)=C[C@@H](c2ccccc2)N1`
ZINC2163720	0.536	229.1 Da LogP -0.41 TPSA 103.7	✓ Ro5	✓ Clean	`O=C(O)C[C@H](NC(=O)C(F)(F)F)C(=O)O`
ZINC2163721	0.536	229.1 Da LogP -0.41 TPSA 103.7	✓ Ro5	✓ Clean	`O=C(O)C[C@@H](NC(=O)C(F)(F)F)C(=O)O`
ZINC238418542	0.536	205.2 Da LogP -1.59 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@@H](O)C(=O)N[C@@H](CC(=O)O)C(=O)O`
ZINC238418655	0.536	205.2 Da LogP -1.59 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@@H](O)C(=O)N[C@H](CC(=O)O)C(=O)O`
ZINC238483548	0.536	205.2 Da LogP -1.59 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](O)C(=O)N[C@@H](CC(=O)O)C(=O)O`
ZINC238483690	0.536	205.2 Da LogP -1.59 TPSA 123.9	✓ Ro5	✓ Clean	`C[C@H](O)C(=O)N[C@H](CC(=O)O)C(=O)O`
ZINC2384834	0.533	232.2 Da LogP -0.99 TPSA 129.7	✓ Ro5	✓ Clean	`CC(C)[C@H](N)C(=O)N[C@@H](CC(=O)O)C(=O)O`
ZINC2560987	0.533	232.2 Da LogP -0.99 TPSA 129.7	✓ Ro5	✓ Clean	`CC(C)[C@@H](N)C(=O)N[C@@H](CC(=O)O)C(=O)O`
ZINC4763075	0.533	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`CC[C@H](N)C(=O)N[C@@H](CC(=O)O)C(=O)O`
ZINC4763081	0.533	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`CC[C@@H](N)C(=O)N[C@@H](CC(=O)O)C(=O)O`
ZINC4763084	0.533	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`CC[C@H](N)C(=O)N[C@H](CC(=O)O)C(=O)O`
ZINC4763089	0.533	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`CC[C@@H](N)C(=O)N[C@H](CC(=O)O)C(=O)O`
ZINC2390918	0.531	261.3 Da LogP -1.51 TPSA 155.7	✓ Ro5	✓ Clean	`NCCCC[C@H](N)C(=O)N[C@@H](CC(=O)O)C(=O)O`
ZINC1087986	0.529	227.2 Da LogP -1.73 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CCNC(=O)c1cc(=O)[nH]c(=O)[nH]1`
ZINC34482669	0.528	224.3 Da LogP 1.22 TPSA 78.4	✓ Ro5	✓ Clean	`O=C1NC(C(=O)O)=C[C@@H](C2CCCCC2)N1`
ZINC34482670	0.528	224.3 Da LogP 1.22 TPSA 78.4	✓ Ro5	✓ Clean	`O=C1NC(C(=O)O)=C[C@H](C2CCCCC2)N1`
ZINC142111850	0.517	247.2 Da LogP -0.71 TPSA 141.0	✓ Ro5	✓ Clean	`O=C(O)CCCC(=O)N[C@@H](CC(=O)O)C(=O)O`
ZINC1731772	0.516	262.2 Da LogP -1.78 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)O)C(=O)N[C@@H](CC(=O)O)C(=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.