Protein profile

KP13_03535

Coproporphyrinogen-III oxidase, aerobic

Genome: KpKP13

Gene: AHE43341.1 hemF Structure source: AlphaFold + ColabFold UniProt A0A0H3GVY6

Export view

Amino acids 299

Annotations 7

Features 29

PDB binders 2

Druggability 0.943

Overview

Basic information about this protein and its source genome.

Accession: KP13_03535
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE43341.1 hemF
Status: annotated
Amino acids: 299
Structure source: AlphaFold + ColabFold

1.3.3.3

GO:0006779 The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group. GO:0004109 Catalysis of the reaction: coproporphyrinogen III + 2 H+ + O2 = 2 CO2 + 2 H2O + protoporphyrinogen IX. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0046872 Binding to a metal ion. GO:0042803 Binding to an identical protein to form a homodimer. GO:0006782 The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 60.0
Human E-value: 4.92e-11
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 73.579
DEG E-value: 1.91e-163
Localization: Cytoplasmic
ColabFold pLDDT: 96.39

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 0.943

Structure A0A0H3GVY6

Pocket Pocket 23

P2Rank 0.986

Structure A0A0H3GVY6

Pocket Pocket 1

ColabFold model

FPocket 0.553 · Pocket 20

P2Rank 0.987 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 165 / 4744 genomes with a hit

Normalized 0.035

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1.3.3.3

Gene Ontology (GO)

GO:0006779 The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.
GO:0004109 Catalysis of the reaction: coproporphyrinogen III + 2 H+ + O2 = 2 CO2 + 2 H2O + protoporphyrinogen IX.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0046872 Binding to a metal ion.
GO:0042803 Binding to an identical protein to form a homodimer.
GO:0006782 The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX.

Sequence Features

Domain/signature hits from InterPro and related databases.

29 records

Show feature table

Start	End	DB	Term	Name
1	299	PIRSF	PIRSF000166	Coproporphyri_ox
1	299	InterPro	IPR001260	Coproporphyrinogen III oxidase, aerobic
1	299	Gene3D	G3DSA:3.40.1500.10	Coproporphyrinogen III oxidase, aerobic
1	299	InterPro	IPR036406	Oxygen-dependent coproporphyrinogen III oxidase superfamily
164	188	ProSitePatterns	PS01021	Coproporphyrinogen III oxidase signature.
164	188	InterPro	IPR018375	Coproporphyrinogen III oxidase, conserved site
5	299	PANTHER	PTHR10755	COPROPORPHYRINOGEN III OXIDASE, MITOCHONDRIAL
5	299	InterPro	IPR001260	Coproporphyrinogen III oxidase, aerobic
123	145	PRINTS	PR00073	Coprogen oxidase signature
123	145	InterPro	IPR001260	Coproporphyrinogen III oxidase, aerobic
46	67	PRINTS	PR00073	Coprogen oxidase signature
46	67	InterPro	IPR001260	Coproporphyrinogen III oxidase, aerobic
88	112	PRINTS	PR00073	Coprogen oxidase signature
88	112	InterPro	IPR001260	Coproporphyrinogen III oxidase, aerobic
29	45	PRINTS	PR00073	Coprogen oxidase signature
29	45	InterPro	IPR001260	Coproporphyrinogen III oxidase, aerobic
160	189	PRINTS	PR00073	Coprogen oxidase signature
160	189	InterPro	IPR001260	Coproporphyrinogen III oxidase, aerobic
260	286	PRINTS	PR00073	Coprogen oxidase signature
260	286	InterPro	IPR001260	Coproporphyrinogen III oxidase, aerobic
232	259	PRINTS	PR00073	Coprogen oxidase signature
232	259	InterPro	IPR001260	Coproporphyrinogen III oxidase, aerobic
4	298	SUPERFAMILY	SSF102886	Coproporphyrinogen III oxidase
4	298	InterPro	IPR036406	Oxygen-dependent coproporphyrinogen III oxidase superfamily
2	275	Hamap	MF_00333	Oxygen-dependent coproporphyrinogen-III oxidase [hemF].
2	275	InterPro	IPR001260	Coproporphyrinogen III oxidase, aerobic
1	299	FunFam	G3DSA:3.40.1500.10:FF:000001	Oxygen-dependent coproporphyrinogen-III oxidase
7	298	Pfam	PF01218	Coproporphyrinogen III oxidase
7	298	InterPro	IPR001260	Coproporphyrinogen III oxidase, aerobic

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...

Legend High Medium Low

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_A0A0H3GVY6	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_03535	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
23				0.943
5				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	44.54	0.972
2	2.41	0.065
3	2.38	0.063

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
20				0.553

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	44.88	0.972
2	2.14	0.05
3	1.19	0.01

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
0PA	3DWR	P84155	128.2 Da LogP 1.65 TPSA 37.3	✓ Ro5	✓ Clean	`C1CCC(C1)CC(=O)O`
FIC	3DWS	P84155	179.1 Da LogP 2.01 TPSA 53.1	✓ Ro5	✓ Clean	`c1cc2c(cc1F)cc([nH]2)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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL2270643	Q42840	8.52	357.3 Da LogP 3.91 TPSA 44.1	✓ Ro5	✓ Clean	`C#CCOc1cc(-n2nc(C(C)(C)C)sc2=O)c(Cl)cc1Cl`

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
ZINC391863	0.778	200.2 Da LogP 1.74 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CC1CCC(CC(=O)O)CC1`
ZINC138516278	0.730	337.3 Da LogP 3.74 TPSA 98.0	✓ Ro5	✓ Clean	`O=C(O)c1cc2cc(NC(=O)c3cc4cc(F)ccc4[nH]3)ccc2[nH…`
ZINC1532902	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC2018106	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
ZINC12869789	0.657	206.2 Da LogP 2.01 TPSA 36.1	✓ Ro5	✓ Clean	`CN(C)C(=O)c1cc2cc(F)ccc2[nH]1`
ZINC2582702	0.656	205.2 Da LogP 1.56 TPSA 90.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc2[nH]c(C(=O)O)cc2c1`
ZINC402742	0.656	240.1 Da LogP 2.63 TPSA 53.1	✓ Ro5	✓ Clean	`O=C(O)c1cc2cc(Br)ccc2[nH]1`
ZINC3593496	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC3593497	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC20028468	0.649	232.3 Da LogP 2.54 TPSA 36.1	✓ Ro5	✓ Clean	`O=C(c1cc2cc(F)ccc2[nH]1)N1CCCC1`
ZINC5268899	0.639	272.3 Da LogP 3.70 TPSA 44.9	✓ Ro5	✓ Clean	`O=C(Nc1ccc(F)cc1)c1cc2cc(F)ccc2[nH]1`
ZINC2122566	0.636	341.2 Da LogP 3.44 TPSA 57.3	✓ Ro5	✓ Clean	`C#CCOc1cc(-n2nc(C(C)(C)C)oc2=O)c(Cl)cc1Cl`
ZINC2432858	0.636	287.1 Da LogP 2.47 TPSA 53.1	✓ Ro5	✓ Clean	`O=C(O)c1cc2cc(I)ccc2[nH]1`
ZINC12888311	0.632	260.3 Da LogP 3.32 TPSA 36.1	✓ Ro5	✓ Clean	`O=C(c1cc2cc(F)ccc2[nH]1)N1CCCCCC1`
ZINC32755156	0.632	246.3 Da LogP 2.93 TPSA 36.1	✓ Ro5	✓ Clean	`O=C(c1cc2cc(F)ccc2[nH]1)N1CCCCC1`
ZINC11956231	0.629	207.2 Da LogP 1.37 TPSA 70.2	✓ Ro5	✓ Clean	`O=C(O)c1cc2cc(F)ccc2[nH]c1=O`
ZINC1420704	0.629	207.2 Da LogP 1.37 TPSA 70.2	✓ Ro5	✓ Clean	`O=C(O)c1cc(=O)c2cc(F)ccc2[nH]1`
ZINC2384078	0.629	229.2 Da LogP 2.88 TPSA 53.1	✓ Ro5	✓ Clean	`O=C(O)c1cc2cc(C(F)(F)F)ccc2[nH]1`
ZINC14686440	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…`
ZINC14686442	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=O…`
ZINC14686444	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=…`
ZINC398906	0.619	200.2 Da LogP 1.74 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)C[C@H]1CCCC[C@@H]1CC(=O)O`
ZINC13007430	0.605	234.3 Da LogP 2.79 TPSA 36.1	✓ Ro5	✓ Clean	`CCN(CC)C(=O)c1cc2cc(F)ccc2[nH]1`
ZINC18736	0.605	207.2 Da LogP 2.48 TPSA 42.1	✓ Ro5	✓ Clean	`CCOC(=O)c1cc2cc(F)ccc2[nH]1`
ZINC20028329	0.605	220.2 Da LogP 2.45 TPSA 44.9	✓ Ro5	✓ Clean	`CC(C)NC(=O)c1cc2cc(F)ccc2[nH]1`
ZINC14985707	0.600	203.2 Da LogP 2.07 TPSA 70.2	✓ Ro5	✓ Clean	`CC(=O)c1ccc2[nH]c(C(=O)O)cc2c1`
ZINC20028330	0.600	261.3 Da LogP 1.69 TPSA 39.3	✓ Ro5	✓ Clean	`CN1CCN(C(=O)c2cc3cc(F)ccc3[nH]2)CC1`
ZINC2582700	0.600	217.3 Da LogP 3.16 TPSA 53.1	✓ Ro5	✓ Clean	`CC(C)(C)c1ccc2[nH]c(C(=O)O)cc2c1`
ZINC32003100	0.600	237.3 Da LogP 3.53 TPSA 53.1	✓ Ro5	✓ Clean	`O=C(O)c1cc2cc(-c3ccccc3)ccc2[nH]1`
ZINC40497239	0.600	268.3 Da LogP 3.58 TPSA 36.1	✓ Ro5	✓ Clean	`CN(C(=O)c1cc2cc(F)ccc2[nH]1)c1ccccc1`
ZINC82862565	0.600	210.2 Da LogP 2.83 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CC1CCC(C(F)(F)F)CC1`
ZINC5346714	0.595	282.3 Da LogP 3.58 TPSA 36.1	✓ Ro5	✓ Clean	`CN(Cc1ccccc1)C(=O)c1cc2cc(F)ccc2[nH]1`
ZINC19685918	0.593	225.3 Da LogP 2.51 TPSA 40.5	✓ Ro5	✓ Clean	`O=C(O)CC1CCN(C2CCCCC2)CC1`
ZINC584905838	0.593	200.4 Da LogP 2.97 TPSA 37.3	✓ Ro5	✓ Clean	`C[Si]1(C)CCC[C@@H](CC(=O)O)CC1`
ZINC584905839	0.593	200.4 Da LogP 2.97 TPSA 37.3	✓ Ro5	✓ Clean	`C[Si]1(C)CCC[C@H](CC(=O)O)CC1`
ZINC12946858	0.590	218.2 Da LogP 2.20 TPSA 44.9	✓ Ro5	✓ Clean	`O=C(NC1CC1)c1cc2cc(F)ccc2[nH]1`
ZINC32779849	0.590	222.2 Da LogP 1.94 TPSA 45.3	✓ Ro5	✓ Clean	`CON(C)C(=O)c1cc2cc(F)ccc2[nH]1`
ZINC13003350	0.585	234.3 Da LogP 2.84 TPSA 44.9	✓ Ro5	✓ Clean	`CC[C@@H](C)NC(=O)c1cc2cc(F)ccc2[nH]1`
ZINC13003352	0.585	234.3 Da LogP 2.84 TPSA 44.9	✓ Ro5	✓ Clean	`CC[C@H](C)NC(=O)c1cc2cc(F)ccc2[nH]1`
ZINC13957077	0.585	344.4 Da LogP 4.83 TPSA 44.9	✓ Ro5	✓ Clean	`O=C(NC(c1ccccc1)c1ccccc1)c1cc2cc(F)ccc2[nH]1`
ZINC5267168	0.585	268.3 Da LogP 3.24 TPSA 44.9	✓ Ro5	✓ Clean	`O=C(NCc1ccccc1)c1cc2cc(F)ccc2[nH]1`
ZINC5345841	0.585	341.4 Da LogP 3.41 TPSA 39.3	✓ Ro5	✓ Clean	`O=C(c1cc2cc(F)ccc2[nH]1)N1CCN(c2ccc(F)cc2)CC1`
ZINC95989650	0.585	262.2 Da LogP 1.65 TPSA 82.2	✓ Ro5	✓ Clean	`O=C(NC1(C(=O)O)CC1)c1cc2cc(F)ccc2[nH]1`
ZINC13821173	0.583	207.2 Da LogP 1.37 TPSA 70.2	✓ Ro5	✓ Clean	`O=C(O)c1cc(=O)c2ccc(F)cc2[nH]1`
ZINC3748658	0.583	203.2 Da LogP 2.99 TPSA 53.1	✓ Ro5	✓ Clean	`CC(C)c1ccc2[nH]c(C(=O)O)cc2c1`
ZINC161561	0.579	245.2 Da LogP 2.76 TPSA 62.3	✓ Ro5	✓ Clean	`O=C(O)c1cc2cc(OC(F)(F)F)ccc2[nH]1`
ZINC13398039	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC2528012	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC12907968	0.575	260.2 Da LogP 2.60 TPSA 44.9	✓ Ro5	✓ Clean	`O=C(NCC(F)(F)F)c1cc2cc(F)ccc2[nH]1`
ZINC12978339	0.575	216.2 Da LogP 1.67 TPSA 44.9	✓ Ro5	✓ Clean	`C#CCNC(=O)c1cc2cc(F)ccc2[nH]1`

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.