Protein profile

KP13_04871

Clavaminate synthase-like superfamily protein

Genome: KpKP13

Gene: AHE45231.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GVM4

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Amino acids 373

Annotations 2

Features 14

PDB binders 5

Druggability 0.862

Overview

Basic information about this protein and its source genome.

Accession: KP13_04871
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE45231.1
Status: annotated
Amino acids: 373
Structure source: AlphaFold + ColabFold

GO:0016706 Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor. GO:0046872 Binding to a metal ion.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 37.5
Human E-value: 7.29e-07
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 86.792
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 96.87

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 0.862

Structure A0A0H3GVM4

Pocket Pocket 2

P2Rank 0.922

Structure A0A0H3GVM4

Pocket Pocket 1

ColabFold model

FPocket 0.639 · Pocket 2

P2Rank 0.926 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 118 / 4744 genomes with a hit

Normalized 0.025

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

GO:0016706 Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor.
GO:0046872 Binding to a metal ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records

Show feature table

Start	End	DB	Term	Name
96	210	Pfam	PF08007	JmjC domain
96	210	InterPro	IPR003347	JmjC domain
205	372	Gene3D	G3DSA:3.40.366.30	50S ribosomal protein L16 arginine hydroxylase; Chain A, Domain 2
92	215	SMART	SM00558	cupin_9
92	215	InterPro	IPR003347	JmjC domain
8	223	PANTHER	PTHR13096	MINA53 MYC INDUCED NUCLEAR ANTIGEN
8	223	InterPro	IPR039994	JmjC domain-containing
257	369	Pfam	PF20514	ROXA-like winged helix
257	369	InterPro	IPR046799	ROXA-like, winged helix
2	204	Gene3D	G3DSA:2.60.120.650	Cupin
2	204	FunFam	G3DSA:2.60.120.650:FF:000012	Cupin superfamily protein family
7	292	SUPERFAMILY	SSF51197	Clavaminate synthase-like
92	219	ProSiteProfiles	PS51184	JmjC domain profile.
92	219	InterPro	IPR003347	JmjC 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_A0A0H3GVM4	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_04871	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
2				0.862

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	24.25	0.897
2	7.63	0.403
3	4.64	0.201
4	2.85	0.089
5	1.97	0.042

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				0.639

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	23.03	0.885
2	6.27	0.314
3	4.79	0.212
4	1.94	0.04
5	1.83	0.035

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.

55 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
AKG	4LIT	P27431	146.1 Da LogP -0.50 TPSA 91.7	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)C(=O)O`
OGA	4CUG	D0MK34	147.1 Da LogP -1.73 TPSA 103.7	✓ Ro5	✓ Clean	`C(C(=O)O)NC(=O)C(=O)O`
PD2	4DIQ	Q9H6W3	167.1 Da LogP 0.48 TPSA 87.5	✓ Ro5	✓ Clean	`c1cnc(cc1C(=O)O)C(=O)O`
SIN	4LIV	P27431	118.1 Da LogP -0.06 TPSA 74.6	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)O`
UN9	4CSW	D0MK34	280.7 Da LogP 1.41 TPSA 99.5	✓ Ro5	✓ Clean	`c1ccc2c(c1)c(c(nc2Cl)C(=O)NCC(=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
ZINC7670	1.000	280.7 Da LogP 1.41 TPSA 99.5	✓ Ro5	✓ Clean	`O=C(O)CNC(=O)c1nc(Cl)c2ccccc2c1O`
ZINC15782053	0.690	227.2 Da LogP 2.01 TPSA 67.3	✓ Ro5	✓ Clean	`O=C(c1ccccc1)c1ccnc(C(=O)O)c1`
ZINC331417	0.690	227.2 Da LogP 2.01 TPSA 67.3	✓ Ro5	✓ Clean	`O=C(O)c1ccnc(C(=O)c2ccccc2)c1`
ZINC38880695	0.680	244.2 Da LogP 1.54 TPSA 100.4	✓ Ro5	✓ Clean	`O=C(O)c1cc(-c2ccnc(C(=O)O)c2)ccn1`
ZINC56644	0.680	244.2 Da LogP 1.54 TPSA 100.4	✓ Ro5	✓ Clean	`O=C(O)c1ccnc(-c2cc(C(=O)O)ccn2)c1`
ZINC35570360	0.667	223.6 Da LogP 2.29 TPSA 70.4	✓ Ro5	✓ Clean	`O=C(O)c1nc(Cl)c2ccccc2c1O`
ZINC166201325	0.656	223.2 Da LogP 1.74 TPSA 76.5	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)c1ccnc(C(=O)O)c1`
ZINC26439009	0.655	243.2 Da LogP 2.15 TPSA 87.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccnc(C(=O)O)c2)cc1`
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`
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(=…`
ZINC390821980	0.625	223.2 Da LogP 1.74 TPSA 76.5	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)c1cc(C(=O)O)ccn1`
ZINC151256	0.607	202.0 Da LogP 1.54 TPSA 50.2	✓ Ro5	✓ Clean	`O=C(O)c1cc(Br)ccn1`
ZINC333016	0.607	249.0 Da LogP 1.38 TPSA 50.2	✓ Ro5	✓ Clean	`O=C(O)c1cc(I)ccn1`
ZINC3866429	0.607	202.0 Da LogP 1.54 TPSA 50.2	✓ Ro5	✓ Clean	`O=C(O)c1ccnc(Br)c1`
ZINC4352682	0.607	249.0 Da LogP 1.38 TPSA 50.2	✓ Ro5	✓ Clean	`O=C(O)c1ccnc(I)c1`
ZINC38342145	0.600	237.6 Da LogP 2.38 TPSA 59.4	✓ Ro5	✓ Clean	`COC(=O)c1nc(Cl)c2ccccc2c1O`
ZINC35654093	0.586	365.3 Da LogP 2.30 TPSA 150.6	✓ Ro5	✓ Clean	`O=C(O)c1ccnc(-c2cc(C(=O)O)cc(-c3cc(C(=O)O)ccn3)…`
ZINC47214440	0.586	200.2 Da LogP 1.84 TPSA 63.1	✓ Ro5	✓ Clean	`O=C(O)c1cc(-c2ccncc2)ccn1`
ZINC47214422	0.581	200.2 Da LogP 1.84 TPSA 63.1	✓ Ro5	✓ Clean	`O=C(O)c1ccnc(-c2ccncc2)c1`
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`
ZINC168888549	0.571	284.3 Da LogP -0.35 TPSA 104.6	✓ Ro5	✓ Clean	`O=C(O)c1cc(C(=O)N2CCS(=O)(=O)CC2)ccn1`
ZINC2598993	0.567	203.2 Da LogP 0.03 TPSA 104.6	✓ Ro5	✓ Clean	`O=C(O)c1cc(S(=O)(=O)O)ccn1`
ZINC146315135	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@@](O)(CC(=O)O)C(=O)O`
ZINC146315336	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@](O)(CC(=O)O)C(=O)O`
ZINC124644877	0.553	264.3 Da LogP 0.81 TPSA 99.5	✓ Ro5	✓ Clean	`O=C(N[C@@H]1CCCC[C@@H]1O)c1ccnc(C(=O)O)c1`
ZINC124645116	0.553	264.3 Da LogP 0.81 TPSA 99.5	✓ Ro5	✓ Clean	`O=C(N[C@H]1CCCC[C@@H]1O)c1ccnc(C(=O)O)c1`
ZINC124645281	0.553	264.3 Da LogP 0.81 TPSA 99.5	✓ Ro5	✓ Clean	`O=C(N[C@@H]1CCCC[C@H]1O)c1ccnc(C(=O)O)c1`
ZINC124645494	0.553	264.3 Da LogP 0.81 TPSA 99.5	✓ Ro5	✓ Clean	`O=C(N[C@H]1CCCC[C@H]1O)c1ccnc(C(=O)O)c1`
ZINC136976573	0.553	250.3 Da LogP 0.69 TPSA 88.5	✓ Ro5	✓ Clean	`O=C(NC1CCOCC1)c1ccnc(C(=O)O)c1`
ZINC1708388	0.548	287.3 Da LogP 3.54 TPSA 47.0	✓ Ro5	✓ Clean	`O=C(c1ccccc1)c1ccnc(C(=O)c2ccccc2)c1`
ZINC20357742	0.548	200.2 Da LogP 1.84 TPSA 63.1	✓ Ro5	✓ Clean	`O=C(O)c1ccnc(-c2ccccn2)c1`
ZINC2598999	0.548	203.2 Da LogP 0.03 TPSA 104.6	✓ Ro5	✓ Clean	`O=C(O)c1ccnc(S(=O)(=O)O)c1`
ZINC38283909	0.548	214.2 Da LogP 2.15 TPSA 63.1	✓ Ro5	✓ Clean	`Cc1ccnc(-c2cc(C(=O)O)ccn2)c1`
ZINC65347060	0.548	213.2 Da LogP 2.76 TPSA 50.2	✓ Ro5	✓ Clean	`Cc1ccc(-c2ccnc(C(=O)O)c2)cc1`
ZINC74941936	0.548	304.3 Da LogP 1.33 TPSA 118.8	✓ Ro5	✓ Clean	`O=C(O)c1ccnc(OCCOc2cc(C(=O)O)ccn2)c1`
ZINC98213921	0.545	207.1 Da LogP 1.68 TPSA 59.4	✓ Ro5	✓ Clean	`O=C(O)c1cc(OC(F)(F)F)ccn1`
ZINC263424469	0.541	220.2 Da LogP 0.92 TPSA 79.3	✓ Ro5	✓ Clean	`C[C@@H]1C[C@H]1NC(=O)c1cc(C(=O)O)ccn1`
ZINC263424470	0.541	220.2 Da LogP 0.92 TPSA 79.3	✓ Ro5	✓ Clean	`C[C@H]1C[C@H]1NC(=O)c1cc(C(=O)O)ccn1`
ZINC263424471	0.541	220.2 Da LogP 0.92 TPSA 79.3	✓ Ro5	✓ Clean	`C[C@@H]1C[C@@H]1NC(=O)c1cc(C(=O)O)ccn1`
ZINC263424472	0.541	220.2 Da LogP 0.92 TPSA 79.3	✓ Ro5	✓ Clean	`C[C@H]1C[C@@H]1NC(=O)c1cc(C(=O)O)ccn1`
ZINC71257465	0.540	352.3 Da LogP 2.86 TPSA 108.8	✓ Ro5	✓ Clean	`Cc1nc(C(=O)NCC(=O)O)c(O)c2ccc(Oc3ccccc3)cc12`
ZINC1595538	0.538	211.1 Da LogP 0.18 TPSA 124.8	✓ Ro5	✓ Clean	`O=C(O)c1cc(C(=O)O)nc(C(=O)O)c1`
ZINC306145916	0.531	241.1 Da LogP 2.43 TPSA 50.2	✓ Ro5	✓ Clean	`O=C(O)c1ccnc(C(F)(F)C(F)(F)F)c1`
ZINC42684404	0.531	201.2 Da LogP 0.18 TPSA 84.3	✓ Ro5	✓ Clean	`CS(=O)(=O)c1cc(C(=O)O)ccn1`
ZINC65348611	0.531	268.1 Da LogP 3.75 TPSA 50.2	✓ Ro5	✓ Clean	`O=C(O)c1cc(-c2ccc(Cl)c(Cl)c2)ccn1`
ZINC79006721	0.531	202.2 Da LogP -0.57 TPSA 110.4	✓ Ro5	✓ Clean	`NS(=O)(=O)c1cc(C(=O)O)ccn1`

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.