Protein profile

KP13_00189

Phosphopantetheine adenylyltransferase

Genome: KpKP13

Gene: AHE42103.1 coaD Structure source: Experimental + ColabFold UniProt Q9XC89
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Amino acids 159
Annotations 7
Features 25
PDB binders 22
Druggability 0.457

Overview

Basic information about this protein and its source genome.

Accession
KP13_00189
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE42103.1 coaD
Status
annotated
Amino acids
159
Structure source
Experimental + ColabFold
EC
2.7.7.3
GO
GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. GO:0015937 The chemical reactions and pathways resulting in the formation of coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester. GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GO:0004595 Catalysis of the reaction: ATP + pantetheine 4'-phosphate = 3'-dephospho-CoA + diphosphate. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
86.164
DEG E-value
1.1100000000000001e-103
Localization
Cytoplasmic
ColabFold pLDDT
96.3

Selected Druggability evidence

PDB experimental structure

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 0.457
Structure 8I8I
Pocket Pocket 1
P2Rank 0.615
Structure 8I8I
Pocket Pocket 1
ColabFold model
FPocket 0.316 · Pocket 2
P2Rank 0.84 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 237 / 4744 genomes with a hit
Normalized 0.05

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

Gene Ontology (GO)

6
  • GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
  • GO:0015937 The chemical reactions and pathways resulting in the formation of coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0004595 Catalysis of the reaction: ATP + pantetheine 4'-phosphate = 3'-dephospho-CoA + diphosphate.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.

Sequence Features

Domain/signature hits from InterPro and related databases.

25 records
Show feature table
Start End DB Term Name
5 63 NCBIfam TIGR00125 cytidyltransferase-like domain
5 63 InterPro IPR004821 Cytidyltransferase-like domain
1 159 FunFam G3DSA:3.40.50.620:FF:000012 Phosphopantetheine adenylyltransferase
3 156 SUPERFAMILY SSF52374 Nucleotidylyl transferase
3 157 PANTHER PTHR21342 PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
3 21 PRINTS PR01020 Lipopolysaccharide core biosynthesis protein signature
3 21 InterPro IPR001980 Phosphopantetheine adenylyltransferase
113 135 PRINTS PR01020 Lipopolysaccharide core biosynthesis protein signature
113 135 InterPro IPR001980 Phosphopantetheine adenylyltransferase
86 102 PRINTS PR01020 Lipopolysaccharide core biosynthesis protein signature
86 102 InterPro IPR001980 Phosphopantetheine adenylyltransferase
21 42 PRINTS PR01020 Lipopolysaccharide core biosynthesis protein signature
21 42 InterPro IPR001980 Phosphopantetheine adenylyltransferase
50 74 PRINTS PR01020 Lipopolysaccharide core biosynthesis protein signature
50 74 InterPro IPR001980 Phosphopantetheine adenylyltransferase
5 157 NCBIfam TIGR01510 pantetheine-phosphate adenylyltransferase
5 157 InterPro IPR001980 Phosphopantetheine adenylyltransferase
6 134 Pfam PF01467 Cytidylyltransferase-like
6 134 InterPro IPR004821 Cytidyltransferase-like domain
3 159 Hamap MF_00151 Phosphopantetheine adenylyltransferase [coaD].
3 159 InterPro IPR001980 Phosphopantetheine adenylyltransferase
1 159 Gene3D G3DSA:3.40.50.620 HUPs
1 159 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
4 156 CDD cd02163 PPAT
4 156 InterPro IPR001980 Phosphopantetheine adenylyltransferase

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

1 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
PDB 8I8I
X-ray 2.59 Å A,B,C
100.0% 1-159
PDBe RCSB PDBj File
Viewing
ColabFold KP13_00189
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
5 0.497
3 0.457
2 0.328
1 0.27

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 12.62 0.657
2 11.82 0.627
3 11.14 0.597
4 2.41 0.065
5 1.64 0.027

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.

72 records

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
ASC
6JOG
A0A059ZFC5 176.1 Da LogP -1.41 TPSA 107.2 ✓ Ro5 ✓ Clean C([C@@H]([C@@H]1C(=C(C(=O)O1)O)O)O)O
COD
1B6T
P0A6I6 687.6 Da LogP -1.78 TPSA 300.0 3 viol. ✓ Clean CC(C)(CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]…
CW4
6B7F
P0A6I6 268.3 Da LogP 3.06 TPSA 44.1 ✓ Ro5 ✓ Clean CC1([C@@H](c2ccccc2C(=O)O1)n3cncc3C=C)C
CWA
6B7E
P0A6I6 292.3 Da LogP 3.36 TPSA 44.1 ✓ Ro5 ✓ Clean CC1([C@@H](c2ccccc2C(=O)O1)n3cncc3C(F)F)C
CWG
6B7D
P0A6I6 248.7 Da LogP 3.42 TPSA 35.0 ✓ Ro5 ✓ Clean Cc1c(c(nnc1c2ccc(cc2)Cl)OC)C
CWJ
6B7B
P0A6I6 161.2 Da LogP 2.48 TPSA 25.0 ✓ Ro5 ✓ Clean Cc1cc2cc(ccc2[nH]1)OC
CWM
6B7A
P0A6I6 148.2 Da LogP 1.58 TPSA 48.9 ✓ Ro5 ✓ Clean Cc1[nH]c2c(n1)cccc2O
CWP
6B7C
P0A6I6 256.3 Da LogP 1.92 TPSA 71.4 ✓ Ro5 ✓ Clean Cc1ccc2c(n1)[nH]c(n2)NCc3cc(nn3C)C
EX7
6CCQ
P0A6I6 272.7 Da LogP 3.71 TPSA 48.9 ✓ Ro5 ✓ Clean c1cc(cc(c1)Cl)CCc2[nH]c3c(n2)cccc3O
EXD
6CCS
P0A6I6 202.1 Da LogP 2.29 TPSA 48.9 ✓ Ro5 ✓ Clean c1cc2c(c(c1)O)[nH]c(n2)C(F)(F)F
EXG
6CCL
P0A6I6 209.3 Da LogP 2.48 TPSA 30.7 ✓ Ro5 ✓ Clean c1ccc(cc1)Cn2cnc3c2cccn3
EXJ
6CCK
P0A6I6 328.8 Da LogP 3.13 TPSA 96.0 ✓ Ro5 ✓ Clean CC1=Nc2nc(nn2C(=O)C1)NC(CC#N)c3cccc(c3)Cl
EXP
6CCM
P0A6I6 334.2 Da LogP 2.79 TPSA 72.2 ✓ Ro5 ✓ Clean CC1=Nc2nc(nn2C(=O)C1)NCc3cccc(c3)Br
EXS
6CCN
P0A6I6 307.4 Da LogP 0.31 TPSA 118.5 ✓ Ro5 ✓ Clean CC(C)(CO)[C@H](C(=O)NCCc1[nH]c2c(n1)cccc2O)O
EXV
6CCO
P0A6I6 322.4 Da LogP 4.02 TPSA 86.2 ✓ Ro5 ✓ Clean c1cc(cc(c1)C(=O)O)[C@H]2CCC[C@@H]2c3[nH]c4c(n3)…
F0V
6CHQ
P0A6I6 364.9 Da LogP 4.15 TPSA 57.7 ✓ Ro5 ✓ Clean Cc1ccc(cc1Cl)Nc2cc(nc3[n+]2nc([nH]3)Cc4ccccc4)C
F0Y
6CHP
P0A6I6 432.5 Da LogP 4.35 TPSA 106.9 ✓ Ro5 ✓ Clean Cc1ccc2c(n1)[nH]c(n2)NC(CC#N)c3cccc(c3)CC4CCN(C…
F14
6CHO
P0A6I6 391.4 Da LogP 4.39 TPSA 90.6 ✓ Ro5 ✓ Clean CC1=Nc2nc(nn2C(=O)C1)N[C@H](C)c3cccc(c3)Oc4ccc(…
F1D
6CHN
P0A6I6 451.5 Da LogP 3.09 TPSA 134.7 ✓ Ro5 ✓ Clean CC1=Nc2nc(nn2C(=O)C1)NC(CC#N)c3cccc(c3)OC4CCN(C…
F1V
6CHM
P0A6I6 274.4 Da LogP 2.88 TPSA 54.1 ✓ Ro5 ✓ Clean CC(C)(C)C(=O)NCCc1c[nH]c2c1cc(cc2)OC
F6D
6CKW
P0A6I6 477.0 Da LogP 4.27 TPSA 126.2 ✓ Ro5 ✓ Clean Cc1cc(n2c(n1)nc(n2)NC(CC#N)c3cccc(c3)Cl)NCC(c4c…
POP
6J3M
A0A059ZFC5 176.0 Da LogP -2.08 TPSA 129.9 ✓ Ro5 ✓ Clean O[P@@](=O)([O-])O[P@@](=O)(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.