Protein profile

KP13_05231

HpxD

Genome: KpKP13

Gene: hpxD AHE44638.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GPR1

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Amino acids 345

Annotations 3

Features 16

PDB binders 8

Druggability 0.92

Overview

Basic information about this protein and its source genome.

Accession: KP13_05231
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: hpxD AHE44638.1
Status: annotated
Amino acids: 345
Structure source: AlphaFold + ColabFold

GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. GO:0005506 Binding to an iron (Fe) ion. GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.

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: 93.56

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 0.92

Structure A0A0H3GPR1

Pocket Pocket 4

P2Rank 0.954

Structure A0A0H3GPR1

Pocket Pocket 1

ColabFold model

FPocket 0.957 · Pocket 2

P2Rank 0.924 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 34 / 4744 genomes with a hit

Normalized 0.007

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
GO:0005506 Binding to an iron (Fe) ion.
GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records

Show feature table

Start	End	DB	Term	Name
26	128	ProSiteProfiles	PS51296	Rieske [2Fe-2S] iron-sulfur domain profile.
26	128	InterPro	IPR017941	Rieske [2Fe-2S] iron-sulphur domain
20	146	Gene3D	G3DSA:2.102.10.10	-
20	146	InterPro	IPR036922	Rieske [2Fe-2S] iron-sulphur domain superfamily
133	338	SUPERFAMILY	SSF55961	Bet v1-like
19	336	PANTHER	PTHR21266	IRON-SULFUR DOMAIN CONTAINING PROTEIN
170	337	Pfam	PF19112	Vanillate O-demethylase oxygenase C-terminal domain
170	337	InterPro	IPR044043	Vanillate O-demethylase oxygenase-like, C-terminal catalytic domain
65	87	ProSitePatterns	PS00570	Bacterial ring hydroxylating dioxygenases alpha-subunit signature.
65	87	InterPro	IPR015881	Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site
14	134	SUPERFAMILY	SSF50022	ISP domain
14	134	InterPro	IPR036922	Rieske [2Fe-2S] iron-sulphur domain superfamily
152	338	Gene3D	G3DSA:3.90.380.10	-
26	135	CDD	cd03469	Rieske_RO_Alpha_N
26	104	Pfam	PF00355	Rieske [2Fe-2S] domain
26	104	InterPro	IPR017941	Rieske [2Fe-2S] iron-sulphur 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_A0A0H3GPR1	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_05231	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
4				0.92
13				0.331

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	34.04	0.948
2	7.81	0.414
3	3.37	0.12
4	1.34	0.015

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
2				0.957

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	25.51	0.907
2	7.11	0.369
3	3.28	0.115
4	1.99	0.042

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
37T	6ICQ	H9N289	180.2 Da LogP -1.04 TPSA 72.7	✓ Ro5	✓ Clean	`Cn1cnc2c1C(=O)NC(=O)N2C`
CFF	6ICN	H9N289	194.2 Da LogP -1.03 TPSA 61.8	✓ Ro5	✓ Clean	`Cn1cnc2c1C(=O)N(C(=O)N2C)C`
D3M	3GB4	Q5S3I3	221.0 Da LogP 2.70 TPSA 46.5	✓ Ro5	✓ Clean	`COc1c(ccc(c1C(=O)O)Cl)Cl`
FES	6WNC	C3RVP5	175.8 Da LogP 1.29 TPSA 0.0	✓ Ro5	✓ Clean	`S1[Fe]S[Fe]1`
HXX	3GOB	Q5S3I3	207.0 Da LogP 2.40 TPSA 57.5	✓ Ro5	✓ Clean	`c1cc(c(c(c1Cl)C(=O)O)O)Cl`
OXY	3GKE	Q5S3I3	32.0 Da LogP 0.07 TPSA 34.1	✓ Ro5	✓ Clean	`O=O`
TEP	6ICO	H9N289	180.2 Da LogP -1.04 TPSA 72.7	✓ Ro5	✓ Clean	`CN1c2c([nH]cn2)C(=O)N(C1=O)C`
U5A	6WND	C3RVP5	267.3 Da LogP -1.72 TPSA 139.4	1 viol.	✓ Clean	`[H]/N=C\1/N[C@H]2[C@@H](N/C(=N/[H])/N3[C@]2(N1)…`

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
ZINC126322	1.000	221.0 Da LogP 2.70 TPSA 46.5	✓ Ro5	✓ Clean	`COc1c(Cl)ccc(Cl)c1C(=O)O`
ZINC2026917	1.000	207.0 Da LogP 2.40 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1c(Cl)ccc(Cl)c1O`
ZINC93099	0.786	216.6 Da LogP 2.06 TPSA 55.8	✓ Ro5	✓ Clean	`COc1ccc(Cl)c(OC)c1C(=O)O`
ZINC49582089	0.759	202.6 Da LogP 1.75 TPSA 66.8	✓ Ro5	✓ Clean	`COc1c(Cl)ccc(O)c1C(=O)O`
ZINC169795993	0.733	265.5 Da LogP 2.81 TPSA 46.5	✓ Ro5	✓ Clean	`COc1c(Br)ccc(Cl)c1C(=O)O`
ZINC212331071	0.733	204.6 Da LogP 2.19 TPSA 46.5	✓ Ro5	✓ Clean	`COc1c(Cl)ccc(F)c1C(=O)O`
ZINC13209773	0.724	210.3 Da LogP 0.34 TPSA 44.8	✓ Ro5	✓ Clean	`Cn1c(=S)c2c(ncn2C)n(C)c1=O`
ZINC5784437	0.714	235.0 Da LogP 2.39 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1c(Cl)ccc(Cl)c1C(=O)O`
ZINC13212548	0.710	222.2 Da LogP 0.01 TPSA 61.8	✓ Ro5	✓ Clean	`CC(C)n1c(=O)n(C)c(=O)c2c1ncn2C`
ZINC1090002	0.700	386.4 Da LogP -2.12 TPSA 123.6	1 viol.	✓ Clean	`Cn1cnc2c1c(=O)n(CCn1c(=O)c3c(ncn3C)n(C)c1=O)c(=…`
ZINC258837921	0.692	251.5 Da LogP 2.51 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1c(Cl)ccc(Br)c1O`
ZINC258839917	0.692	251.5 Da LogP 2.51 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1c(Br)ccc(Cl)c1O`
ZINC2516178	0.690	235.1 Da LogP 2.79 TPSA 35.5	✓ Ro5	✓ Clean	`COC(=O)c1c(Cl)ccc(Cl)c1OC`
ZINC13212541	0.688	208.2 Da LogP -0.55 TPSA 61.8	✓ Ro5	✓ Clean	`CCn1c(=O)n(C)c(=O)c2c1ncn2C`
ZINC93126	0.679	251.1 Da LogP 2.71 TPSA 55.8	✓ Ro5	✓ Clean	`COc1c(Cl)cc(Cl)c(OC)c1C(=O)O`
ZINC34090877	0.677	372.3 Da LogP -2.31 TPSA 123.6	1 viol.	✓ Clean	`Cn1cnc2c1c(=O)n(Cn1c(=O)c3c(ncn3C)n(C)c1=O)c(=O…`
ZINC1090003	0.667	386.4 Da LogP -2.12 TPSA 123.6	1 viol.	✓ Clean	`Cn1c(=O)c2c(ncn2CCn2cnc3c2c(=O)n(C)c(=O)n3C)n(C…`
ZINC12405449	0.667	222.2 Da LogP -0.16 TPSA 61.8	✓ Ro5	✓ Clean	`CCCn1c(=O)n(C)c(=O)c2c1ncn2C`
ZINC9975012	0.656	400.4 Da LogP -1.73 TPSA 123.6	1 viol.	✓ Clean	`Cn1cnc2c1c(=O)n(CCCn1c(=O)c3c(ncn3C)n(C)c1=O)c(…`
ZINC12604163	0.649	400.4 Da LogP -1.73 TPSA 123.6	1 viol.	✓ Clean	`Cn1c(=O)c2c(ncn2CCCn2c(=O)c3c(ncn3C)n(C)c2=O)n(…`
ZINC13212543	0.647	224.2 Da LogP -1.57 TPSA 82.1	✓ Ro5	✓ Clean	`Cn1c(=O)c2c(ncn2C)n(CCO)c1=O`
ZINC13212557	0.647	236.3 Da LogP 0.23 TPSA 61.8	✓ Ro5	✓ Clean	`CCCCn1c(=O)n(C)c(=O)c2c1ncn2C`
ZINC13212561	0.647	236.3 Da LogP 0.09 TPSA 61.8	✓ Ro5	✓ Clean	`CC(C)Cn1c(=O)n(C)c(=O)c2c1ncn2C`
ZINC18816333	0.645	222.2 Da LogP 0.01 TPSA 61.8	✓ Ro5	✓ Clean	`CC(C)n1cnc2c1c(=O)n(C)c(=O)n2C`
ZINC13284606	0.636	222.2 Da LogP -0.16 TPSA 61.8	✓ Ro5	✓ Clean	`CCCn1c(=O)c2c(ncn2C)n(C)c1=O`
ZINC1666589	0.629	250.3 Da LogP 0.48 TPSA 61.8	✓ Ro5	✓ Clean	`CC(C)CCn1c(=O)c2c(ncn2C)n(C)c1=O`
ZINC224909	0.629	208.2 Da LogP -0.17 TPSA 72.7	✓ Ro5	✓ Clean	`CCCn1cnc2c1c(=O)[nH]c(=O)n2C`
ZINC1069064	0.625	400.4 Da LogP -1.73 TPSA 123.6	1 viol.	✓ Clean	`Cn1c(=O)c2c(ncn2CCCn2cnc3c2c(=O)n(C)c(=O)n3C)n(…`
ZINC15865845	0.625	208.2 Da LogP -0.55 TPSA 61.8	✓ Ro5	✓ Clean	`CCn1cnc2c1c(=O)n(C)c(=O)n2C`
ZINC1849975	0.625	225.5 Da LogP 3.35 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1c(Cl)ccc(Cl)c1Cl`
ZINC20593730	0.625	223.0 Da LogP 2.10 TPSA 77.8	✓ Ro5	✓ Clean	`O=C(O)c1c(O)c(Cl)cc(Cl)c1O`
ZINC37866048	0.625	414.4 Da LogP -1.34 TPSA 123.6	1 viol.	✓ Clean	`Cn1c(=O)c2c(ncn2CCCCn2cnc3c2c(=O)n(C)c(=O)n3C)n…`
ZINC15909445	0.622	242.2 Da LogP 0.41 TPSA 72.7	✓ Ro5	✓ Clean	`Cn1c(=O)c2[nH]cnc2n(-c2ccccc2)c1=O`
ZINC3861807	0.622	222.2 Da LogP 0.08 TPSA 72.7	✓ Ro5	✓ Clean	`CC(C)Cn1c(=O)n(C)c(=O)c2[nH]cnc21`
ZINC485783	0.622	237.3 Da LogP -1.02 TPSA 75.9	✓ Ro5	✓ Clean	`CN(C)CCn1c(=O)c2[nH]cnc2n(C)c1=O`
ZINC2918225	0.618	279.1 Da LogP 2.24 TPSA 72.8	✓ Ro5	✓ Clean	`COc1c(Cl)ccc(Cl)c1C(=O)OCC(=O)O`
ZINC36056255	0.615	207.0 Da LogP 2.40 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1c(Cl)ccc(O)c1Cl`
ZINC2038718	0.613	255.5 Da LogP 3.35 TPSA 46.5	✓ Ro5	✓ Clean	`COc1c(Cl)cc(Cl)c(Cl)c1C(=O)O`
ZINC212303686	0.613	202.6 Da LogP 1.75 TPSA 66.8	✓ Ro5	✓ Clean	`COc1c(Cl)ccc(C(=O)O)c1O`
ZINC35065830	0.613	221.0 Da LogP 2.70 TPSA 46.5	✓ Ro5	✓ Clean	`COc1c(Cl)ccc(C(=O)O)c1Cl`
ZINC85210443	0.613	221.0 Da LogP 2.70 TPSA 46.5	✓ Ro5	✓ Clean	`COc1ccc(Cl)c(C(=O)O)c1Cl`
ZINC13216239	0.611	234.3 Da LogP 0.18 TPSA 61.8	✓ Ro5	✓ Clean	`C=C[C@H](C)n1c(=O)c2c(ncn2C)n(C)c1=O`
ZINC13283559	0.611	234.3 Da LogP 0.18 TPSA 61.8	✓ Ro5	✓ Clean	`C=C[C@@H](C)n1c(=O)c2c(ncn2C)n(C)c1=O`
ZINC266363	0.606	206.2 Da LogP -0.47 TPSA 61.8	✓ Ro5	✓ Clean	`C=Cn1cnc2c1c(=O)n(C)c(=O)n2C`
ZINC380547	0.606	222.2 Da LogP -0.16 TPSA 61.8	✓ Ro5	✓ Clean	`CCCn1cnc2c1c(=O)n(C)c(=O)n2C`
ZINC94778	0.606	262.1 Da LogP 3.14 TPSA 38.3	✓ Ro5	✓ Clean	`COc1c(Cl)ccc(Cl)c1C(=O)NC(C)C`
ZINC95915995	0.606	249.1 Da LogP 3.18 TPSA 35.5	✓ Ro5	✓ Clean	`CCOC(=O)c1c(Cl)ccc(Cl)c1OC`
ZINC164509468	0.605	238.2 Da LogP -1.10 TPSA 110.0	✓ Ro5	✓ Clean	`Cn1c(=O)n(CCC(=O)O)c(=O)c2[nH]cnc21`
ZINC485643	0.605	237.3 Da LogP -1.02 TPSA 75.9	✓ Ro5	✓ Clean	`CN(C)CCn1c(=O)[nH]c(=O)c2c1ncn2C`
ZINC5491033	0.605	237.3 Da LogP -1.02 TPSA 75.9	✓ Ro5	✓ Clean	`CN(C)CCn1c(=O)n(C)c(=O)c2[nH]cnc21`

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.