Protein profile

KP13_31515

Long-chain-fatty-acid--CoA ligase

Genome: KpKP13

Gene: AHE43908.1 fadD Structure source: AlphaFold + ColabFold UniProt A0A0H3GRT5

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Amino acids 572

Annotations 0

Features 15

PDB binders 12

Druggability 0.217

Overview

Basic information about this protein and its source genome.

Accession: KP13_31515
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE43908.1 fadD
Status: annotated
Amino acids: 572
Structure source: AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 42.0
Human E-value: 2.88e-07
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 92.03

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 0.217

Structure A0A0H3GRT5

Pocket Pocket 27

P2Rank 0.808

Structure A0A0H3GRT5

Pocket Pocket 1

ColabFold model

FPocket 0.624 · Pocket 31

P2Rank 0.982 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 253 / 4744 genomes with a hit

Normalized 0.053

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

No GO or EC annotations are currently loaded for this protein.

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records

Show feature table

Start	End	DB	Term	Name
467	569	Gene3D	G3DSA:3.30.300.30	-
467	569	InterPro	IPR045851	AMP-binding enzyme, C-terminal domain superfamily
466	567	FunFam	G3DSA:3.30.300.30:FF:000006	Long-chain-fatty-acid--CoA ligase FadD
22	466	Gene3D	G3DSA:3.40.50.12780	-
22	466	InterPro	IPR042099	ANL, N-terminal domain
21	466	FunFam	G3DSA:3.40.50.12780:FF:000003	Long-chain-fatty-acid--CoA ligase FadD
222	233	ProSitePatterns	PS00455	Putative AMP-binding domain signature.
222	233	InterPro	IPR020845	AMP-binding, conserved site
36	561	CDD	cd05936	FC-FACS_FadD_like
480	554	Pfam	PF13193	AMP-binding enzyme C-terminal domain
480	554	InterPro	IPR025110	AMP-binding enzyme, C-terminal domain
28	566	PANTHER	PTHR43767	LONG-CHAIN-FATTY-ACID--COA LIGASE
40	471	Pfam	PF00501	AMP-binding enzyme
40	471	InterPro	IPR000873	AMP-dependent synthetase/ligase domain
22	566	SUPERFAMILY	SSF56801	Acetyl-CoA synthetase-like

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_A0A0H3GRT5	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_31515	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
27				0.217

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	12.16	0.641
2	2.85	0.089
3	1.86	0.037
4	1.69	0.029
5	1.41	0.018

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
31				0.624

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	34.99	0.952
2	4.04	0.162
3	2.69	0.08
4	0.98	0.005
5	0.78	0.002

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.

62 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
3SK	4RLQ	Q93TK0	136.2 Da LogP 1.69 TPSA 37.3	✓ Ro5	✓ Clean	`Cc1ccccc1C(=O)O`
3U4	4RM2	Q93TK0	140.1 Da LogP 1.52 TPSA 37.3	✓ Ro5	✓ Clean	`c1ccc(c(c1)C(=O)O)F`
3UK	4WV3	F3Y661	466.3 Da LogP -0.42 TPSA 218.2	1 viol.	✓ Clean	`c1ccc(c(c1)C(=O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([…`
4MA	4RLF	Q93TK0	136.2 Da LogP 1.69 TPSA 37.3	✓ Ro5	✓ Clean	`Cc1ccc(cc1)C(=O)O`
4UU	5BST	O24146	493.4 Da LogP -0.30 TPSA 209.2	1 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
4UV	5BSU	O24146	507.4 Da LogP -1.12 TPSA 226.3	2 viol.	Alert	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
4UW	5BSV	O24146	523.4 Da LogP -0.33 TPSA 218.4	2 viol.	✓ Clean	`COC1=CC(=CCC1=O)/C=C/C(=O)OP(=O)(O)OC[C@@H]2[C@…`
AYL	3NI2	Q941M3	481.4 Da LogP 0.50 TPSA 195.3	1 viol.	✓ Clean	`c1cc(ccc1CCCO[P@](=O)(O)OC[C@@H]2[C@H]([C@H]([C…`
BEZ	4EAT	Q93TK0	122.1 Da LogP 1.38 TPSA 37.3	✓ Ro5	✓ Clean	`c1ccc(cc1)C(=O)O`
FOA	4RM3	Q93TK0	112.1 Da LogP 0.98 TPSA 50.4	✓ Ro5	✓ Clean	`c1cc(oc1)C(=O)O`
JSA	5ZRN	P9WQ37	530.6 Da LogP 1.12 TPSA 194.9	2 viol.	✓ Clean	`CCCCCCCCCCC[C@H](NS(=O)(=O)OC[C@@H]1[C@H]([C@H]…`
MLI	3R44	P9WQ37	102.0 Da LogP -3.12 TPSA 80.3	✓ Ro5	✓ Clean	`C(C(=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
ZINC2565512	0.895	212.2 Da LogP 3.36 TPSA 37.3	✓ Ro5	✓ Clean	`Cc1ccc(-c2ccc(C(=O)O)cc2)cc1`
ZINC3269660	0.824	254.2 Da LogP 2.45 TPSA 71.4	✓ Ro5	Alert	`O=C(O)c1ccc(C(=O)C(=O)c2ccccc2)cc1`
ZINC2504355	0.778	226.2 Da LogP 2.62 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccccc2)cc1`
ZINC66672	0.750	240.3 Da LogP 2.92 TPSA 54.4	✓ Ro5	✓ Clean	`Cc1ccccc1C(=O)c1ccccc1C(=O)O`
ZINC100251304	0.739	240.3 Da LogP 4.11 TPSA 62.0	✓ Ro5	Alert	`Cc1ccc(/N=N\c2ccc(C(=O)O)cc2)cc1`
ZINC1601396	0.739	228.2 Da LogP 3.49 TPSA 46.5	✓ Ro5	✓ Clean	`Cc1ccc(Oc2ccc(C(=O)O)cc2)cc1`
ZINC1667194	0.739	254.3 Da LogP 4.02 TPSA 37.3	✓ Ro5	✓ Clean	`Cc1ccc(C(C)(C)c2ccc(C(=O)O)cc2)cc1`
ZINC197528838	0.739	226.3 Da LogP 3.28 TPSA 37.3	✓ Ro5	✓ Clean	`Cc1ccc(Cc2ccc(C(=O)O)cc2)cc1`
ZINC4742441	0.739	240.3 Da LogP 4.11 TPSA 62.0	✓ Ro5	Alert	`Cc1ccc(/N=N/c2ccc(C(=O)O)cc2)cc1`
ZINC31539924	0.729	494.4 Da LogP -0.74 TPSA 218.2	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OC(=O…`
ZINC1593172	0.708	276.3 Da LogP 2.53 TPSA 71.4	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC1672966	0.688	210.2 Da LogP 2.75 TPSA 34.1	✓ Ro5	Alert	`O=C(C(=O)c1ccccc1)c1ccccc1`
ZINC134079	0.684	242.2 Da LogP 2.75 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(C(=O)O)cc2)cc1`
ZINC1590056	0.684	238.3 Da LogP 3.37 TPSA 34.1	✓ Ro5	Alert	`Cc1ccc(C(=O)C(=O)c2ccc(C)cc2)cc1`
ZINC3147211	0.684	318.3 Da LogP 4.42 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(-c3ccc(C(=O)O)cc3)cc2)cc1`
ZINC34057267	0.684	274.3 Da LogP 4.72 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(-c3ccccc3)cc2)cc1`
ZINC12360002	0.682	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12360703	0.682	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12503599	0.682	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC1596373	0.682	210.3 Da LogP 3.53 TPSA 17.1	✓ Ro5	✓ Clean	`Cc1ccccc1C(=O)c1ccccc1C`
ZINC16546165	0.682	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@](=O)(O)OP(=O)(…`
ZINC1705669	0.682	238.3 Da LogP 3.37 TPSA 34.1	✓ Ro5	Alert	`Cc1ccccc1C(=O)C(=O)c1ccccc1C`
ZINC1847557	0.682	218.2 Da LogP 3.20 TPSA 17.1	✓ Ro5	✓ Clean	`O=C(c1ccccc1F)c1ccccc1F`
ZINC28713881	0.682	246.2 Da LogP 3.03 TPSA 34.1	✓ Ro5	Alert	`O=C(C(=O)c1ccccc1F)c1ccccc1F`
ZINC31977053	0.682	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC4806433	0.682	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC53683898	0.682	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586019	0.682	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC8586020	0.682	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586021	0.682	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC8586022	0.682	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC2580772	0.680	212.2 Da LogP 3.36 TPSA 37.3	✓ Ro5	✓ Clean	`Cc1ccccc1-c1ccccc1C(=O)O`
ZINC397456	0.680	270.3 Da LogP 3.34 TPSA 78.4	✓ Ro5	✓ Clean	`Cc1ccc(NC(=O)Nc2ccc(C(=O)O)cc2)cc1`
ZINC4299204	0.680	216.2 Da LogP 3.19 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1-c1ccccc1F`
ZINC13518964	0.672	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515	0.672	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC1571045	0.672	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC1842158	0.672	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC2046931	0.672	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.672	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891	0.672	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893	0.672	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.672	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.672	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.672	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O…`
ZINC4806442	0.672	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC8613167	0.672	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC1713131	0.667	270.3 Da LogP 3.37 TPSA 74.6	✓ Ro5	✓ Clean	`Cc1cccc(C(=O)O)c1-c1c(C)cccc1C(=O)O`
ZINC221605357	0.667	332.4 Da LogP 4.73 TPSA 74.6	✓ Ro5	✓ Clean	`Cc1cc(-c2ccc(C(=O)O)cc2)cc(-c2ccc(C(=O)O)cc2)c1`
ZINC4204244	0.667	226.3 Da LogP 3.67 TPSA 37.3	✓ Ro5	✓ Clean	`Cc1cc(C)cc(-c2ccc(C(=O)O)cc2)c1`

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.