Protein profile

PA2399

pyoverdine synthetase D

Genome: NC_002516.2

Gene: PA2399 pvdD Structure source: AlphaFold UniProt Q9I182
Export view
Amino acids 2448
Annotations 9
Features 87
PDB binders 14
Druggability 0.726

Overview

Basic information about this protein and its source genome.

Accession
PA2399
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA2399 pvdD
Status
annotated
Amino acids
2448
Structure source
AlphaFold
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. 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:0016874 Catalysis of the joining of two molecules, or two groups within a single molecule, using the energy from the hydrolysis of ATP, a similar triphosphate, or a pH gradient. GO:0031177 Binding to phosphopantetheine, the vitamin pantetheine 4'-(dihydrogen phosphate). GO:0043041 Activation of an amino acid for incorporation into a peptide by a nonribosomal process.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
30.667
Human E-value
1.66e-06
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

Selected Druggability evidence

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 0.726
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MQALIEKVGSLSPQERKALAVLLKQQGVNLFEIAPVFKRQDGEPLRLSYAQERQWFLWQLEPESAAYHIPSVLRLRGRLDLDALQRSFDSLVARHETLRTRFRLDGDEARQEIAASMALPLDIVALGPLEEGALARQVETTIARPFDLERGPLLRVSLLRLAEDDHVLVLVQHHIVSDGWSMQVMVEELVQLYAAYSRGLEVALPALPIQYADYALWQRSWMEAGEKERQLAYWTGLLGGEQPVLELPFDRPRPVRQSHRGAQFILELDIDLSQALRRVAQQEGATAFALLLASFQALLYRYSGQADIRVGVPIANRNRVETERLIGFFVNTQVLKADLDGRMGFDELLAQARQRALEAQAHQDLPFEQLVEALQPERSLSHNPLFQVLFNYQSEARGNGQAFRFDELQMESVQFDSRTAQFDLTLDLTDEEQRFCAVFDYATDLFDASTVERLAGHWRNLLRGIVANPRQRLGELPLLDAPERRQTLSEWNPAQRECAVQGTLQQRFEEQARQRPQAVALILDEQRLSYGELNARANRLAHCLIARGVGADVPVGLALERSLDMLVGLLAILKAGGAYLPLDPAAPEERLAHILDDSGVRLLLTQGHLLERLPRQAGVEVLAIDGLVLDGYAESDPLPTLSADNLAYVIYTSGSTGKPKGTLLTHRNALRLFSATEAWFGFDERDVWTLFHSYAFDFSVWEIFGALLYGGCLVIVPQWVSRSPEDFYRLLCREGVTVLNQTPSAFKQLMAVACSADMATQQPALRYVIFGGEALDLQSLRPWFQRFGDRQPQLVNMYGITETTVHVTYRPVSEADLEGGLVSPIGGTIPDLSWYILDRDLNPVPRGAVGELYIGRAGLARGYLRRPGLSATRFVPNPFPGGAGERLYRTGDLARFQADGNIEYIGRIDHQVKVRGFRIELGEIEAALAGLAGVRDAVVLAHDGVGGTQLVGYVVADSAEDAERLRESLRESLKRHLPDYMVPAHLMLLERMPLTVNGKLDRQALPQPDASLSQQAYRAPGSELEQRIAAIWSEILGVERVGLDDNFFELGGHSLLATRVISRVRQEQQLDASLKALFERPVLEAFAQGLERTTDAVSTIPLADRQQPLALSFAQERQWFLWQLEPESAAYHIPSALRLRGRLDVDALQRSFDSLVARHETLRTRFRLEGGRSYQQVQPAVSVSIEREQFGEEGLIERIQAIVVQPFDLERGPLLRVNLLQLAEDDHVLVLVQHHIVSDGWSMQVMVEELVQLYAAYSQGLDVVLPALPIQYADYALWQRSWMEAGEKERQLAYWTGLLGGEQPVLELPFDRPRPARQSHRGAQLGFELSRELVEAVRALAQREGASSFMLLLASFQALLYRYSGQADIRVGVPIANRNRVETERLIGFFVNTQVLKADLDGRMGFDELLAQARQRALEAQAHQDLPFEQLVEALQPERNASHNPLFQVLFNHQSEIRSVTPEVQLEDLRLEGLAWDGQTAQFDLTLDIQEDENGIWASFDYATDLFDASTVERLAGHWRNLLRGIVANPRQRLGELPLLDAPERRQTLSEWNPAQRECAVQGTLQQRFEEQARQRPQAVALILDEQRLSYGELNARANRLAHCLIARGVGADVPVGLALERSLDMLVGLLAILKAGGAYLPLDPAAPEERLAHILDDSGVRLLLTQGHLLERLPRQAGVEVLAIDGLVLDGYAESDPLPTLSADNLAYVIYTSGSTGKPKGTLLTHRNALRLFSATEAWFGFDERDVWTLFHSYAFDFSVWEIFGALLYGGRLVIVPQWVSRSPEDFYRLLCREGVTVLNQTPSAFKQLMAVACSADMATQQPALRYVIFGGEALDLQSLRPWFQRFGDRQPQLVNMYGITETTVHVTYRPVSEADLKGGLVSPIGGTIPDLSWYILDRDLNPVPRGAVGELYIGRAGLARGYLRRPGLSATRFVPNPFPGGAGERLYRTGDLARFQADGNIEYIGRIDHQVKVRGFRIELGEIEAALAGLAGVRDAVVLAHDGVGGTQLVGYVVADSAEDAERLRESLRESLKRHLPDYMVPAHLMLLERMPLTVNGKLDRQALPQPDASLSQQAYRAPGSELEQRIAAIWAEILGVERVGLDDNFFELGGHSLLLLMLKERIGDTCQATLSISQLMTHASVAEQAACIEGQARESLLVPLNGRREGSPLFMFHPSFGSVHCYKTLAMALRDRHPVKGVVCRALLGAGREVPEWDDMVAEYAEQLLQEHPEGVFNLAGWSLGGNLAMDVAARLEQRGRQVAFVGWIDAPAPVRVEAFWNEIGPTPEAVPNLSVGEMRVELLGVMFPERAEHIERAWSSICSATTDDEQRWTRMSDWAEAEIGAEFATLRSEIAQSNELEVSWELKQILDERLKAMDYPRLTAKVSLWWAARSTNAIQRSAVERSMAEAIGAERVEPVRVLDTRHDKIIDHPEFVQSFRAALERAGR

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

9 GO

Gene Ontology (GO)

9
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • 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:0016874 Catalysis of the joining of two molecules, or two groups within a single molecule, using the energy from the hydrolysis of ATP, a similar triphosphate, or a pH gradient.
  • GO:0031177 Binding to phosphopantetheine, the vitamin pantetheine 4'-(dihydrogen phosphate).
  • GO:0043041 Activation of an amino acid for incorporation into a peptide by a nonribosomal process.
  • GO:0002049 The chemical reactions and pathways resulting in the formation of the siderochrome pyoverdine.
  • GO:0044550 The chemical reactions and pathways resulting in the formation of secondary metabolites, the compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

87 records
Show feature table
Start End DB Term Name
224 472 Gene3D G3DSA:3.30.559.30 Nonribosomal peptide synthetase, condensation domain
47 220 SUPERFAMILY SSF52777 CoA-dependent acyltransferases
2171 2428 Pfam PF00975 Thioesterase domain
2171 2428 InterPro IPR001031 Thioesterase
2159 2447 Gene3D G3DSA:3.40.50.1820 alpha/beta hydrolase
2159 2447 InterPro IPR029058 Alpha/Beta hydrolase fold
1285 1533 Gene3D G3DSA:3.30.559.30 Nonribosomal peptide synthetase, condensation domain
1025 1094 SMART SM00823 Phosphopantetheine attachment site
1025 1094 InterPro IPR020806 Polyketide synthase, phosphopantetheine-binding domain
2086 2155 SMART SM00823 Phosphopantetheine attachment site
2086 2155 InterPro IPR020806 Polyketide synthase, phosphopantetheine-binding domain
530 661 FunFam G3DSA:3.40.50.980:FF:000001 Non-ribosomal peptide synthetase
1017 1090 SUPERFAMILY SSF47336 ACP-like
1017 1090 InterPro IPR036736 ACP-like superfamily
516 1005 CDD cd17643 A_NRPS_Cytc1-like
226 493 SUPERFAMILY SSF52777 CoA-dependent acyltransferases
1563 1969 FunFam G3DSA:3.40.50.12780:FF:000012 Non-ribosomal peptide synthetase
1591 1722 FunFam G3DSA:3.40.50.980:FF:000001 Non-ribosomal peptide synthetase
502 908 FunFam G3DSA:3.40.50.12780:FF:000012 Non-ribosomal peptide synthetase
1710 1721 ProSitePatterns PS00455 Putative AMP-binding domain signature.
1710 1721 InterPro IPR020845 AMP-binding, conserved site
1016 1093 FunFam G3DSA:1.10.1200.10:FF:000005 Nonribosomal peptide synthetase 1
1285 1473 FunFam G3DSA:3.30.559.30:FF:000001 Non-ribosomal peptide synthetase
2078 2152 SUPERFAMILY SSF47336 ACP-like
2078 2152 InterPro IPR036736 ACP-like superfamily
2077 2158 Gene3D G3DSA:1.10.1200.10 -
2077 2158 InterPro IPR036736 ACP-like superfamily
1016 1096 Gene3D G3DSA:1.10.1200.10 -
1016 1096 InterPro IPR036736 ACP-like superfamily
1019 1094 ProSiteProfiles PS50075 Carrier protein (CP) domain profile.
1019 1094 InterPro IPR009081 Phosphopantetheine binding ACP domain
43 246 PANTHER PTHR45527 NONRIBOSOMAL PEPTIDE SYNTHETASE
465 1038 SUPERFAMILY SSF56801 Acetyl-CoA synthetase-like
649 660 ProSitePatterns PS00455 Putative AMP-binding domain signature.
649 660 InterPro IPR020845 AMP-binding, conserved site
1526 2099 SUPERFAMILY SSF56801 Acetyl-CoA synthetase-like
2080 2155 ProSiteProfiles PS50075 Carrier protein (CP) domain profile.
2080 2155 InterPro IPR009081 Phosphopantetheine binding ACP domain
1287 1554 SUPERFAMILY SSF52777 CoA-dependent acyltransferases
2155 2439 SUPERFAMILY SSF53474 alpha/beta-Hydrolases
2155 2439 InterPro IPR029058 Alpha/Beta hydrolase fold
1577 2066 CDD cd17643 A_NRPS_Cytc1-like
1111 1298 FunFam G3DSA:3.30.559.10:FF:000012 Non-ribosomal peptide synthetase
1723 1886 FunFam G3DSA:3.40.50.980:FF:000002 Enterobactin synthetase component F
1563 1969 Gene3D G3DSA:3.40.50.12780 -
1563 1969 InterPro IPR042099 ANL, N-terminal domain
502 908 Gene3D G3DSA:3.40.50.12780 -
502 908 InterPro IPR042099 ANL, N-terminal domain
909 1013 FunFam G3DSA:3.30.300.30:FF:000010 Enterobactin synthetase component F
1106 1547 Pfam PF00668 Condensation domain
1106 1547 InterPro IPR001242 Condensation domain
46 486 Pfam PF00668 Condensation domain
46 486 InterPro IPR001242 Condensation domain
1970 2076 Gene3D G3DSA:3.30.300.30 -
1970 2076 InterPro IPR045851 AMP-binding enzyme, C-terminal domain superfamily
909 1015 Gene3D G3DSA:3.30.300.30 -
909 1015 InterPro IPR045851 AMP-binding enzyme, C-terminal domain superfamily
44 469 CDD cd19531 LCL_NRPS-like
662 825 FunFam G3DSA:3.40.50.980:FF:000002 Enterobactin synthetase component F
1569 1976 Pfam PF00501 AMP-binding enzyme
1569 1976 InterPro IPR000873 AMP-dependent synthetase/ligase domain
508 915 Pfam PF00501 AMP-binding enzyme
508 915 InterPro IPR000873 AMP-dependent synthetase/ligase domain
2087 2151 Pfam PF00550 Phosphopantetheine attachment site
2087 2151 InterPro IPR009081 Phosphopantetheine binding ACP domain
1026 1088 Pfam PF00550 Phosphopantetheine attachment site
1026 1088 InterPro IPR009081 Phosphopantetheine binding ACP domain
1970 2074 FunFam G3DSA:3.30.300.30:FF:000010 Enterobactin synthetase component F
1108 1530 CDD cd19531 LCL_NRPS-like
1590 2000 NCBIfam TIGR01733 amino acid adenylation domain
1590 2000 InterPro IPR010071 Amino acid adenylation domain
529 939 NCBIfam TIGR01733 amino acid adenylation domain
529 939 InterPro IPR010071 Amino acid adenylation domain
1111 1281 SUPERFAMILY SSF52777 CoA-dependent acyltransferases
224 412 FunFam G3DSA:3.30.559.30:FF:000001 Non-ribosomal peptide synthetase
47 417 Gene3D G3DSA:3.30.559.10 -
47 417 InterPro IPR023213 Chloramphenicol acetyltransferase-like domain superfamily
47 237 FunFam G3DSA:3.30.559.10:FF:000012 Non-ribosomal peptide synthetase
1049 1064 ProSitePatterns PS00012 Phosphopantetheine attachment site.
1049 1064 InterPro IPR006162 Phosphopantetheine attachment site
2077 2154 FunFam G3DSA:1.10.1200.10:FF:000005 Nonribosomal peptide synthetase 1
923 999 Pfam PF13193 AMP-binding enzyme C-terminal domain
923 999 InterPro IPR025110 AMP-binding enzyme, C-terminal domain
1984 2060 Pfam PF13193 AMP-binding enzyme C-terminal domain
1984 2060 InterPro IPR025110 AMP-binding enzyme, C-terminal domain
1111 1478 Gene3D G3DSA:3.30.559.10 -
1111 1478 InterPro IPR023213 Chloramphenicol acetyltransferase-like domain superfamily

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

Loading 3D structure...

Legend High Medium Low

Structural evidence

0 + 1

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA2399
AlphaFold — — full sequence — Viewing
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
1 0.414

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.

64 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
5FQ
5DUA
Q9Z4X6 158.2 Da LogP 0.64 TPSA 55.1 ✓ Ro5 ✓ Clean CCCCCNC(=O)[C@H](C)N
5S4
5ES8
Q70LM7 440.4 Da LogP -1.80 TPSA 200.3 1 viol. ✓ Clean CC(C)[C@@H](C(=O)NCCNC(=O)CCNC(=O)[C@@H](C(C)(C…
9EF
6MFX
Q70LM7 383.3 Da LogP -1.76 TPSA 174.3 1 viol. ✓ Clean CC(=O)NCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)…
APC
5ES7
Q70LM7 505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
CO8
7C1R
E5ATN9 893.7 Da LogP 1.03 TPSA 363.6 3 viol. ✓ Clean CCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P…
DG9
6MG0
Q70LM7 785.8 Da LogP -2.85 TPSA 336.7 3 viol. ✓ Clean CC(C)[C@H]([C@H](CS(=O)(=O)NC[C@@H]1[C@H]([C@H]…
FGU
7C1S
E5ATN9 232.3 Da LogP 0.76 TPSA 72.2 ✓ Ro5 ✓ Clean CC(C)C[C@@H](C(=O)SCCNC(=O)C)N
FLC
6P1J
A0A0B5H0S3 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
FON
5ES7
Q70LM7 473.4 Da LogP -0.73 TPSA 219.8 1 viol. ✓ Clean c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC[C@@H]2…
JQG
6MFW
Q70LM7 468.4 Da LogP -1.84 TPSA 200.2 1 viol. ✓ Clean CC(C)[C@@H](C(=O)NCCNC(=O)CCNC(=O)[C@@H](C(C)(C…
KH4
4PWV
F2YRY5 452.4 Da LogP -0.60 TPSA 190.9 1 viol. ✓ Clean CC(C)(COP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCSC(=O)c…
KIV
6ULZ
Q70LM7 116.1 Da LogP 0.30 TPSA 54.4 ✓ Ro5 ✓ Clean CC(C)C(=O)C(=O)O
PNS
5ES9
Q70LM7 358.4 Da LogP -0.96 TPSA 145.2 1 viol. ✓ Clean CC(C)(COP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCS)O
UM2
5DU9
Q9Z4X6 144.2 Da LogP 0.25 TPSA 55.1 ✓ Ro5 ✓ Clean CCCCNC(=O)[C@H](C)N

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.