Protein profile

VK055_2800

ornithine carbamoyltransferase

Genome: KpATCC43816

Gene: AIK81389.1 argF Structure source: Experimental + ColabFold UniProt A0A0H3GHJ1

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Amino acids 334

Annotations 9

Features 36

PDB binders 15

Druggability 0.453

Overview

Basic information about this protein and its source genome.

Accession: VK055_2800
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK81389.1 argF
Status: annotated
Amino acids: 334
Structure source: Experimental + ColabFold

2.1.3.3

GO:0016743 Catalysis of the transfer of a carboxyl- or carbamoyl group from one compound (donor) to another (acceptor). GO:0006591 The chemical reactions and pathways involving ornithine, an amino acid only rarely found in proteins, but which is important in living organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis. GO:0016597 Binding to an amino acid, organic acids containing one or more amino substituents. GO:0004585 Catalysis of the reaction: carbamoyl phosphate + L-ornithine = phosphate + L-citrulline. GO:0006520 The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 36.89
Human E-value: 2.9500000000000004e-56
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 38.298
Localization: Cytoplasmic
ColabFold pLDDT: 96.21

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 0.453

Structure 7TMD

Pocket Pocket 1

P2Rank 0.436

Structure 7TMD

Pocket Pocket 1

ColabFold model

FPocket 0.922 · Pocket 1

P2Rank 0.699 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 1998 / 4744 genomes with a hit

Normalized 0.421

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

2.1.3.3

Gene Ontology (GO)

GO:0016743 Catalysis of the transfer of a carboxyl- or carbamoyl group from one compound (donor) to another (acceptor).
GO:0006591 The chemical reactions and pathways involving ornithine, an amino acid only rarely found in proteins, but which is important in living organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis.
GO:0016597 Binding to an amino acid, organic acids containing one or more amino substituents.
GO:0004585 Catalysis of the reaction: carbamoyl phosphate + L-ornithine = phosphate + L-citrulline.
GO:0006520 The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0019240 The chemical reactions and pathways resulting in the formation of citrulline, N5-carbamoyl-L-ornithine, an alpha amino acid not found in proteins.
GO:0042450 OBSOLETE. The chemical reactions and pathways resulting in the formation of arginine (2-amino-5-guanidinopentanoic acid) via the intermediate compound ornithine.

Sequence Features

Domain/signature hits from InterPro and related databases.

36 records

Show feature table

Start	End	DB	Term	Name
6	332	Gene3D	G3DSA:3.40.50.1370	Aspartate/ornithine carbamoyltransferase
6	332	InterPro	IPR036901	Aspartate/ornithine carbamoyltransferase superfamily
229	239	PRINTS	PR00102	Ornithine carbamoyltransferase signature
229	239	InterPro	IPR002292	Ornithine/putrescine carbamoyltransferase
83	96	PRINTS	PR00102	Ornithine carbamoyltransferase signature
83	96	InterPro	IPR002292	Ornithine/putrescine carbamoyltransferase
123	137	PRINTS	PR00102	Ornithine carbamoyltransferase signature
123	137	InterPro	IPR002292	Ornithine/putrescine carbamoyltransferase
50	64	PRINTS	PR00102	Ornithine carbamoyltransferase signature
50	64	InterPro	IPR002292	Ornithine/putrescine carbamoyltransferase
311	322	PRINTS	PR00102	Ornithine carbamoyltransferase signature
311	322	InterPro	IPR002292	Ornithine/putrescine carbamoyltransferase
152	319	FunFam	G3DSA:3.40.50.1370:FF:000004	Ornithine carbamoyltransferase
52	71	PRINTS	PR00100	Aspartate/ornithine carbamoyltransferase superfamily signature
52	71	InterPro	IPR006130	Aspartate/ornithine carbamoyltransferase
134	145	PRINTS	PR00100	Aspartate/ornithine carbamoyltransferase superfamily signature
134	145	InterPro	IPR006130	Aspartate/ornithine carbamoyltransferase
297	320	PRINTS	PR00100	Aspartate/ornithine carbamoyltransferase superfamily signature
297	320	InterPro	IPR006130	Aspartate/ornithine carbamoyltransferase
267	276	PRINTS	PR00100	Aspartate/ornithine carbamoyltransferase superfamily signature
267	276	InterPro	IPR006130	Aspartate/ornithine carbamoyltransferase
7	147	Pfam	PF02729	Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
7	147	InterPro	IPR006132	Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding
156	330	Pfam	PF00185	Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
156	330	InterPro	IPR006131	Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain
152	319	Gene3D	G3DSA:3.40.50.1370	Aspartate/ornithine carbamoyltransferase
152	319	InterPro	IPR036901	Aspartate/ornithine carbamoyltransferase superfamily
7	332	NCBIfam	TIGR00658	ornithine carbamoyltransferase
7	332	InterPro	IPR002292	Ornithine/putrescine carbamoyltransferase
2	333	SUPERFAMILY	SSF53671	Aspartate/ornithine carbamoyltransferase
2	333	InterPro	IPR036901	Aspartate/ornithine carbamoyltransferase superfamily
6	333	Hamap	MF_01109	Ornithine carbamoyltransferase, catabolic [argI].
6	333	InterPro	IPR024904	Ornithine carbamoyltransferase
52	59	ProSitePatterns	PS00097	Aspartate and ornithine carbamoyltransferases signature.
52	59	InterPro	IPR006130	Aspartate/ornithine carbamoyltransferase
3	333	PANTHER	PTHR45753	ORNITHINE CARBAMOYLTRANSFERASE, MITOCHONDRIAL

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 7TMD	X-ray	2.35 Å	A,B,C,D,E,F	100.0% 1-334	PDBe RCSB PDBj File	Viewing
ColabFold VK055_2800	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
8				0.756
7				0.567
11				0.474
10				0.219

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	12.9	0.666
2	11.87	0.629
3	11.19	0.6
4	9.71	0.522
5	8.57	0.458

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				0.922

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				9.13	0.489

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.

65 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
1NP	7NNY	P9WIT9	144.2 Da LogP 2.55 TPSA 20.2	✓ Ro5	✓ Clean	`c1ccc2c(c1)cccc2O`
8H8	7NOR	P9WIT9	137.1 Da LogP 1.40 TPSA 44.0	✓ Ro5	✓ Clean	`c1cc(c(cc1O)F)C#N`
98T	7NNW	P9WIT9	278.0 Da LogP 1.78 TPSA 46.5	✓ Ro5	✓ Clean	`COC(=O)c1ccc(c(c1)I)O`
CIR	4JQO	Q8DCF5	175.2 Da LogP -1.15 TPSA 118.4	✓ Ro5	✓ Clean	`C(C[C@@H](C(=O)O)N)CNC(=O)N`
CP	4H31	Q8DCF5	141.0 Da LogP -0.83 TPSA 109.9	✓ Ro5	✓ Clean	`C(=O)(N)OP(=O)(O)O`
NMR	7NOU	P9WIT9	—	—	—	`B(=O)(c1cc(cc(c1)Cl)Cl)O`
NVA	4NF2	Q81M99	117.1 Da LogP 0.20 TPSA 63.3	✓ Ro5	✓ Clean	`CCC[C@@H](C(=O)O)N`
PAO	2OTC	P04391	254.2 Da LogP -1.53 TPSA 149.9	✓ Ro5	✓ Clean	`C(C[C@@H](C(=O)O)N)CNC(=O)CP(=O)(O)O`
PE5	4H31	Q8DCF5	398.5 Da LogP 0.13 TPSA 94.1	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCOCCO`
PSQ	1DUV	P04391	290.2 Da LogP -1.77 TPSA 184.8	1 viol.	✓ Clean	`C(C[C@@H](C(=O)O)N)CN[P@](=O)(N)NS(=O)(=O)O`
PTZ	7NNZ	P9WIT9	190.3 Da LogP 2.70 TPSA 38.9	✓ Ro5	✓ Clean	`Cc1c(nc(s1)N)c2ccccc2`
PUW	4A8H	Q837U7	210.2 Da LogP -0.98 TPSA 112.7	✓ Ro5	✓ Clean	`C(CCNC(=O)CP(=O)(O)O)CN`
UJZ	7NOS	P9WIT9	265.0 Da LogP 3.34 TPSA 28.7	✓ Ro5	✓ Clean	`c1c(cc(c2c1[nH]cn2)Br)C(F)(F)F`
UK2	7NOV	P9WIT9	181.0 Da LogP -0.42 TPSA 83.6	✓ Ro5	✓ Clean	`B(c1ccc(c(c1)[N+](=O)[O-])C)(O)O`
UKH	7NP0	P9WIT9	166.9 Da LogP -0.73 TPSA 83.6	✓ Ro5	✓ Clean	`B(c1ccc(cc1)[N+](=O)[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
ZINC2548331	1.000	278.0 Da LogP 1.78 TPSA 46.5	✓ Ro5	✓ Clean	`COC(=O)c1ccc(O)c(I)c1`
ZINC5650743	1.000	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC6403917	1.000	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC20340495	0.926	266.4 Da LogP 4.37 TPSA 38.9	✓ Ro5	✓ Clean	`Cc1sc(N)nc1-c1ccc(-c2ccccc2)cc1`
ZINC84123	0.750	204.3 Da LogP 3.01 TPSA 38.9	✓ Ro5	Alert	`Cc1ccc(-c2nc(N)sc2C)cc1`
ZINC8700304	0.733	278.0 Da LogP 1.78 TPSA 46.5	✓ Ro5	✓ Clean	`COC(=O)c1ccc(I)c(O)c1`
ZINC258828063	0.719	204.1 Da LogP 2.72 TPSA 28.7	✓ Ro5	✓ Clean	`Fc1cc(C(F)(F)F)cc2[nH]cnc12`
ZINC2032126	0.714	244.3 Da LogP 4.85 TPSA 20.2	✓ Ro5	✓ Clean	`Oc1cccc2c1ccc1c3ccccc3ccc21`
ZINC12501520	0.688	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC3874716	0.688	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC41656314	0.688	204.3 Da LogP 3.01 TPSA 38.9	✓ Ro5	✓ Clean	`Cc1cccc(-c2nc(N)sc2C)c1`
ZINC4283769	0.688	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	0.688	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829	0.688	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	0.688	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5859031	0.688	294.4 Da LogP 1.13 TPSA 55.4	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCC`
ZINC1009200	0.677	208.3 Da LogP 2.84 TPSA 38.9	✓ Ro5	✓ Clean	`Cc1sc(N)nc1-c1ccc(F)cc1`
ZINC115331	0.677	269.2 Da LogP 3.46 TPSA 38.9	✓ Ro5	✓ Clean	`Cc1sc(N)nc1-c1ccc(Br)cc1`
ZINC2528189	0.677	320.1 Da LogP 1.86 TPSA 52.6	✓ Ro5	✓ Clean	`COC(=O)c1ccc(C(=O)OC)c(I)c1`
ZINC2559798	0.677	276.1 Da LogP 2.39 TPSA 26.3	✓ Ro5	✓ Clean	`COC(=O)c1ccc(C)c(I)c1`
ZINC28014904	0.677	206.3 Da LogP 2.41 TPSA 59.1	✓ Ro5	✓ Clean	`Cc1sc(N)nc1-c1ccc(O)cc1`
ZINC7580	0.677	224.7 Da LogP 3.35 TPSA 38.9	✓ Ro5	✓ Clean	`Cc1sc(N)nc1-c1ccc(Cl)cc1`
ZINC1570993	0.667	215.3 Da LogP 2.93 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCC[C@H](N)C(=O)O`
ZINC1570999	0.667	229.4 Da LogP 3.32 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCC[C@H](N)C(=O)O`
ZINC1620974	0.667	243.4 Da LogP 3.71 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[C@H](N)C(=O)O`
ZINC1742220	0.667	201.3 Da LogP 2.54 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCC[C@H](N)C(=O)O`
ZINC2035155	0.667	215.3 Da LogP 2.93 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCC[C@@H](N)C(=O)O`
ZINC2035157	0.667	201.3 Da LogP 2.54 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCC[C@@H](N)C(=O)O`
ZINC2037129	0.667	243.4 Da LogP 3.71 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[C@@H](N)C(=O)O`
ZINC39951743	0.667	292.1 Da LogP 2.17 TPSA 46.5	✓ Ro5	✓ Clean	`CCOC(=O)c1ccc(O)c(I)c1`
ZINC43531622	0.667	271.4 Da LogP 4.49 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC[C@H](N)C(=O)O`
ZINC43531626	0.667	271.4 Da LogP 4.49 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC[C@@H](N)C(=O)O`
ZINC8437446	0.667	229.4 Da LogP 3.32 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCC[C@@H](N)C(=O)O`
ZINC128850	0.656	292.1 Da LogP 2.09 TPSA 35.5	✓ Ro5	✓ Clean	`COC(=O)c1ccc(OC)c(I)c1`
ZINC140445837	0.656	294.1 Da LogP 2.37 TPSA 26.3	✓ Ro5	✓ Clean	`COC(=O)c1ccc(S)c(I)c1`
ZINC21304461	0.656	296.5 Da LogP 2.73 TPSA 26.3	✓ Ro5	✓ Clean	`COC(=O)c1ccc(Cl)c(I)c1`
ZINC2506007	0.656	246.4 Da LogP 4.00 TPSA 38.9	✓ Ro5	✓ Clean	`Cc1sc(N)nc1-c1ccc(C(C)(C)C)cc1`
ZINC393290	0.656	277.1 Da LogP 1.66 TPSA 52.3	✓ Ro5	✓ Clean	`COC(=O)c1ccc(N)c(I)c1`
ZINC4069950	0.656	220.3 Da LogP 2.71 TPSA 48.1	✓ Ro5	✓ Clean	`COc1ccc(-c2nc(N)sc2C)cc1`
ZINC44172055	0.656	280.0 Da LogP 2.22 TPSA 26.3	✓ Ro5	✓ Clean	`COC(=O)c1ccc(F)c(I)c1`
ZINC89064429	0.656	340.9 Da LogP 2.84 TPSA 26.3	✓ Ro5	✓ Clean	`COC(=O)c1ccc(Br)c(I)c1`
ZINC38888013	0.655	403.9 Da LogP 2.39 TPSA 46.5	✓ Ro5	✓ Clean	`COC(=O)c1cc(I)c(O)c(I)c1`
ZINC40162867	0.655	254.2 Da LogP 3.88 TPSA 12.9	✓ Ro5	✓ Clean	`Cc1sc(Br)nc1-c1ccccc1`
ZINC150355	0.647	224.7 Da LogP 3.35 TPSA 38.9	✓ Ro5	✓ Clean	`Cc1sc(N)nc1-c1cccc(Cl)c1`
ZINC41656350	0.647	208.3 Da LogP 2.84 TPSA 38.9	✓ Ro5	✓ Clean	`Cc1sc(N)nc1-c1cccc(F)c1`
ZINC84915946	0.647	269.2 Da LogP 3.46 TPSA 38.9	✓ Ro5	✓ Clean	`Cc1sc(N)nc1-c1cccc(Br)c1`
ZINC404023	0.645	210.2 Da LogP 0.97 TPSA 72.8	✓ Ro5	✓ Clean	`COC(=O)c1ccc(O)c(C(=O)OC)c1`
ZINC2471419	0.636	266.4 Da LogP 4.37 TPSA 38.9	✓ Ro5	✓ Clean	`Cc1ccc(-c2nc(N)sc2-c2ccccc2)cc1`
ZINC39951739	0.636	290.1 Da LogP 2.64 TPSA 26.3	✓ Ro5	✓ Clean	`CCc1ccc(C(=O)OC)cc1I`
ZINC39951741	0.636	291.1 Da LogP 2.12 TPSA 38.3	✓ Ro5	✓ Clean	`CNc1ccc(C(=O)OC)cc1I`

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.