Protein profile

KP13_02905

Protein csiD

Genome: KpKP13

Gene: csiD AHE46182.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GNR6

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Amino acids 338

Annotations 6

Features 9

PDB binders 3

Druggability 0.947

Overview

Basic information about this protein and its source genome.

Accession: KP13_02905
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: csiD AHE46182.1
Status: annotated
Amino acids: 338
Structure source: AlphaFold + ColabFold

1.14.11.64

GO:0005506 Binding to an iron (Fe) ion. GO:0050498 Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and the latter donor is dehydrogenated. GO:0008198 Binding to a ferrous iron ion, Fe(II). GO:0106343 Catalysis of the reaction glutarate + 2-oxoglutarate + O2 = (S)-2-hydroxyglutarate + succinate + CO2. GO:0019477 The chemical reactions and pathways resulting in the breakdown of L-lysine.

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: Unknown
ColabFold pLDDT: 90.39

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 0.947

Structure A0A0H3GNR6

Pocket Pocket 8

P2Rank 0.94

Structure A0A0H3GNR6

Pocket Pocket 1

ColabFold model

FPocket 0.997 · Pocket 13

P2Rank 0.938 · 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.

1 EC 5 GO

Enzyme Commission (EC)

1.14.11.64

Gene Ontology (GO)

GO:0005506 Binding to an iron (Fe) ion.
GO:0050498 Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and the latter donor is dehydrogenated.
GO:0008198 Binding to a ferrous iron ion, Fe(II).
GO:0106343 Catalysis of the reaction glutarate + 2-oxoglutarate + O2 = (S)-2-hydroxyglutarate + succinate + CO2.
GO:0019477 The chemical reactions and pathways resulting in the breakdown of L-lysine.

Sequence Features

Domain/signature hits from InterPro and related databases.

9 records

Show feature table

Start	End	DB	Term	Name
30	331	SUPERFAMILY	SSF51197	Clavaminate synthase-like
73	327	CDD	cd00250	CAS_like
28	338	Gene3D	G3DSA:3.60.130.10	-
28	338	InterPro	IPR042098	Taurine dioxygenase TauD-like superfamily
34	327	Pfam	PF08943	CsiD
34	327	InterPro	IPR015038	Glutarate 2-hydroxylase GlaH
14	338	Hamap	MF_01083	Glutarate 2-hydroxylase [glaH].
14	338	InterPro	IPR015038	Glutarate 2-hydroxylase GlaH
28	338	FunFam	G3DSA:3.60.130.10:FF:000004	Glutarate 2-hydroxylase

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_A0A0H3GNR6	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02905	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				0.947

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				25.48	0.907
2				2.44	0.066

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
13				0.997

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				27.55	0.921
2				3.11	0.105

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
GUA	6HL8	P76621	132.1 Da LogP 0.33 TPSA 74.6	✓ Ro5	✓ Clean	`C(CC(=O)O)CC(=O)O`
OGA	6GPN	P76621	147.1 Da LogP -1.73 TPSA 103.7	✓ Ro5	✓ Clean	`C(C(=O)O)NC(=O)C(=O)O`
SIN	6HL9	P76621	118.1 Da LogP -0.06 TPSA 74.6	✓ Ro5	✓ Clean	`C(CC(=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
ZINC1703342	0.786	202.2 Da LogP 1.07 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCC(=O)CCCC(=O)O`
ZINC1529497	0.769	230.3 Da LogP 3.06 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCC(=O)O`
ZINC1531045	0.769	202.2 Da LogP 2.28 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)O`
ZINC1593115	0.769	216.3 Da LogP 2.67 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCC(=O)O`
ZINC1700020	0.769	244.3 Da LogP 3.45 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCC(=O)O`
ZINC3860440	0.769	258.4 Da LogP 3.84 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCC(=O)O`
ZINC3861298	0.769	286.4 Da LogP 4.62 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCC(=O)O`
ZINC5113062	0.769	272.4 Da LogP 4.23 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCC(=O)O`
ZINC3074815	0.688	230.3 Da LogP 1.85 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCC(=O)CCCC(=O)O`
ZINC2508031	0.667	230.3 Da LogP 1.85 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCC(=O)CCCCC(=O)O`
ZINC4828816	0.647	217.2 Da LogP 1.33 TPSA 107.2	✓ Ro5	✓ Clean	`O=C(O)CCCC(CCCC(=O)O)=NO`
ZINC26897400	0.625	286.4 Da LogP 3.41 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCC(=O)CCCCCCC(=O)O`
ZINC3074813	0.625	258.3 Da LogP 2.63 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCC(=O)CCCCCC(=O)O`
ZINC34423725	0.625	342.5 Da LogP 4.97 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)CCCCCCCCC(=O)O`
ZINC4822898	0.625	272.3 Da LogP 3.02 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCC(=O)CCCCCC(=O)O`
ZINC4822900	0.625	300.4 Da LogP 3.80 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)CCCCCC(=O)O`
ZINC13433578	0.588	201.3 Da LogP 1.68 TPSA 80.4	✓ Ro5	✓ Clean	`NC(=O)CCCCCCCCC(=O)O`
ZINC14510370	0.588	244.4 Da LogP 3.74 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCO`
ZINC1531061	0.588	216.3 Da LogP 2.96 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCO`
ZINC1610426	0.588	230.3 Da LogP 3.35 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCO`
ZINC2168567	0.588	202.3 Da LogP 2.57 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCO`
ZINC3861297	0.588	272.4 Da LogP 4.52 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCCO`
ZINC4284502	0.588	258.4 Da LogP 4.13 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCO`
ZINC5287109	0.588	286.5 Da LogP 4.91 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCCCO`
ZINC98175207	0.579	290.3 Da LogP 0.58 TPSA 127.2	✓ Ro5	✓ Clean	`O=C(O)CCCC(=O)OCCOC(=O)CCCC(=O)O`
ZINC1572706	0.563	260.2 Da LogP -1.05 TPSA 132.8	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)NCCNC(=O)CCC(=O)O`
ZINC115371230	0.556	266.4 Da LogP 2.88 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCSSCCCCC(=O)O`
ZINC12954423	0.556	232.4 Da LogP 3.90 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCS`
ZINC13357569	0.556	243.4 Da LogP 3.71 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCC(=O)O`
ZINC138216182	0.556	293.2 Da LogP 4.76 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCBr`
ZINC14619253	0.556	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCCC(=O)O`
ZINC1529498	0.556	200.3 Da LogP 3.99 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)O`
ZINC1530417	0.556	228.4 Da LogP 4.77 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)O`
ZINC1628119	0.556	214.3 Da LogP 4.38 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)O`
ZINC1661158	0.556	234.3 Da LogP 2.23 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCSCCCCC(=O)O`
ZINC1763117	0.556	201.3 Da LogP 2.54 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCC(=O)O`
ZINC1841307	0.556	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCCCC(=O)O`
ZINC1845814	0.556	215.3 Da LogP 2.93 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCCC(=O)O`
ZINC1845839	0.556	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCC(=O)O`
ZINC2164257	0.556	218.4 Da LogP 3.51 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCS`
ZINC22048354	0.556	229.4 Da LogP 3.32 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCC(=O)O`
ZINC33822328	0.556	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCCCCCCC(=O)O`
ZINC34552398	0.556	257.4 Da LogP 4.10 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCC(=O)O`
ZINC34628306	0.556	271.4 Da LogP 4.49 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCCC(=O)O`
ZINC35465466	0.556	244.3 Da LogP 2.24 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCC(=O)CCC(=O)O`
ZINC5855130	0.556	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCCCCC(=O)O`
ZINC90745150	0.556	260.4 Da LogP 4.68 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCS`
ZINC1728397	0.533	233.2 Da LogP -0.29 TPSA 115.1	✓ Ro5	✓ Clean	`O=C(O)CCN(CCC(=O)O)CCC(=O)O`
ZINC2517013	0.533	250.2 Da LogP 0.89 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)CCP(CCC(=O)O)CCC(=O)O`
ZINC39208104	0.529	262.2 Da LogP -0.20 TPSA 127.2	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)OCCOC(=O)CCC(=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.