Protein profile

PA2400

pyoverdine biosynthesis protein PvdJ

Genome: NC_002516.2

Gene: pvdJ PA2400 Structure source: AlphaFold UniProt Q9I181
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Amino acids 2157
Annotations 9
Features 83
PDB binders 14
Druggability 0.72

Overview

Basic information about this protein and its source genome.

Accession
PA2400
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
pvdJ PA2400
Status
annotated
Amino acids
2157
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:0009366 A multienzyme complex usually composed of four proteins, EntB, EntD, EntE and EntF. Plays a role in the enterobactin biosynthesis pathway. GO:0047527 Catalysis of the reaction: ATP + 2,3-dihydroxybenzoate + L-serine = products of ATP breakdown + N-(2,3-dihydroxybenzoyl)-L-serine. 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:0031177 Binding to phosphopantetheine, the vitamin pantetheine 4'-(dihydrogen phosphate).

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
30.476
Human E-value
2.33e-09
Gut microbiome off-target
hit
Essential (DEG)
N
Localization
Unknown

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 0.72
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MSFARLPIPQTRQEMDNLPLSYAQERQWFLWQLEPESSAYHIPTALRLRGRLDIASLQRSFAALVERHESLRTRIARMGDEWVQVVSADVSLALEVEVQRGLDEQRLLERVEAEIARPFDLEQGPLLRVTLLEVDADEHVLVMVQHHIVSDGWSMQLMVEELVQLYAAYSQGLDVVLPALPIQYADYALWQRSWMEAGEKERQLAYWTGLLGGEQPVIELPLDHPRQPLRSYRGAQLDLELEPHLALALKQLVQRKGVTMFMLLLASFQALLHRYSGQADIRVGVPIANRNRVETERLIGFFVNTQVLKADINGRMGFDELLAQARQRALEAQAHQDLPFEQLVEALQPERSLGHNPLFQVMFNHQADSRSANQGVQLPGLSLERMEWRSSSVAFDLTLDVHEAEDGIWASFGYATDLFEASTVERLARHWQNLLRGIVAEPGRPVAELPLLLDEERDCLSRAWAENADEGGLPPLVQLQIQEQARLRPQAQALALEGQALSYAELNARANRLAHCLIARGVGPDVLVGIAVERSLDMVVGLLAILKAGGAYVPLDPTYPQDRLRHMLEDSAVGLLLSQEHLLPGLPLHEGLEVLSIDRLERDASVSTDDPVVNLRPENLAYVIYTSGSTGKPKGVAISHAALAQFSRIASGYSALTPEDRILQFATLSFDGFVEQLYPALTRGACVVLRGGDLWDTGELYRQIVEQGVTLADLPTAYWNLFLLDALAEPRRSYGALRQIHIGGEAMPLEGPKLWRQAGMGRVRLLNTYGPTEATVVSSVFDCSAENARVGNASPIGQALPGRTLLVLDEHLGLLPVGPVGELYIASRAGLARAYHDRPGLTAERFLPDPFGEPGSRLYRTGDLARRRGDGVIEYMGRADHQVKIRGFRIELGEVEARLLDLEGIREAAALALDGQLVAYLVAEGGEDETRQPALRERIRTALRASLPDYMVPSHLLFLERMPLSPNGKLDRRALPKPDAGLMQRDHMAPASALEKDVAAIWGELLGVERVGLTDNFFELGGHSLLATRLVSRIRQDLGIEVSLKSLFEQPVLQGFVESLGEKPAEVPPITPVTREQPLPLSYAQERQWFLWQLEPESAAYHIPAALRLRGGLDVVALQRSFERLAQRHESLRTRFRQEGLRTVQVVDADGQLQVSRHNLANVDDASLRAAVEAEMARPFDLRTDALLRISLFEVAPNDHVLVMVQHHIVSDGWSMQLMVEELVQLYAAYSQGREAALPALPIQYPDYAVWQREWMEAGERERQLAYWIGLLGGEQPVLELPFDRPRPAEQSFRGARLEFELGAERARRLKALAQRQGASTFMLLLASFQALLYRYSGQSDIRVGVPVANRNRVETERLIGFFVNTQVLKADIDGQMGFDRLLHQVRQRSLEAQAHQDLPFEQLVEALQPERSLSHSPLFQVLFNYQAERGEHGLPEVAGLSIEEQAWESHTAQFDLVLDTCESESDIWAALVYATDLFDASTAERLVRHWQNLLDAILAMPDARLGELDMLDREEREVIGQLWNRSDSGYPATPLVHQRVAERARMAPDAVAVIFDEEKLTYAELDNRANRLAHALIARGVGPEVRVAIAMQRSAEIMVAFLAVLKAGGAYVPLDIEYPRERLLYMMQDSRAHLLLTHSHLLERLPIPEGLSCLSVDREEEWAGFPAHDPEVALHGDNLAYVIYTSGSTGMPKGVAVSHGPLIAHIVATGERYEMTPEDCELHFMSFAFDGSHEGWMHPLINGARVLIRDDSLWLPERTYAEMHRHGVTVGVFPPVYLQQLAEHAERDGNPPPVRVYCFGGDAVAQASYDLAWRALKPKYLFNGYGPTETVVTPLLWKARAGDACGAAYMPIGTLLGNRSGYILDGQLNLLPVGVAGELYLGGEGVARGYLERPALTAERFVPDPFGAPGSRLYRSGDLTRGRADGVVDYLGRVDHQVKIRGFRIELGEIEARLREHPAVREAVVVAQPGAVGQQLVGYVVAQEPAVADSPEAQAECRAQLKTALRERLPEYMVPSHLLFLARMPLTPNGKLDRKGLPQPDASLLQQVYVAPRSDLEQQVAGIWAEVLQLQQVGLDDNFFELGGHSLLATQVIGRLRERLHLEVPIKSMFTAETLGEFCHGVETLKAESAPVEDALAKSLEALKRLSADELEKLIS

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:0009366 A multienzyme complex usually composed of four proteins, EntB, EntD, EntE and EntF. Plays a role in the enterobactin biosynthesis pathway.
  • GO:0047527 Catalysis of the reaction: ATP + 2,3-dihydroxybenzoate + L-serine = products of ATP breakdown + N-(2,3-dihydroxybenzoyl)-L-serine.
  • 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: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:0009239 The chemical reactions and pathways resulting in the formation of enterobactin, a catechol-derived siderochrome of Enterobacteria; enterobactin (N',N',N''-(2,6,10-trioxo-1,5,9-triacyclodecane-3,7,11-triyl)tris(2,3-dihydroxy)benzamide) is a self-triester of 2,3-dihydroxy-N-benzoyl-L-serine and a product of the shikimate pathway.
  • GO:0002049 The chemical reactions and pathways resulting in the formation of the siderochrome pyoverdine.

Sequence Features

Domain/signature hits from InterPro and related databases.

83 records
Show feature table
Start End DB Term Name
485 798 Gene3D G3DSA:3.40.50.980 -
1542 1942 Pfam PF00501 AMP-binding enzyme
1542 1942 InterPro IPR000873 AMP-dependent synthetase/ligase domain
482 886 Pfam PF00501 AMP-binding enzyme
482 886 InterPro IPR000873 AMP-dependent synthetase/ligase domain
2049 2126 FunFam G3DSA:1.10.1200.10:FF:000005 Nonribosomal peptide synthetase 1
197 444 Gene3D G3DSA:3.30.559.30 Nonribosomal peptide synthetase, condensation domain
439 1008 SUPERFAMILY SSF56801 Acetyl-CoA synthetase-like
1078 1502 CDD cd19531 LCL_NRPS-like
1936 2046 Gene3D G3DSA:3.30.300.30 -
1936 2046 InterPro IPR045851 AMP-binding enzyme, C-terminal domain superfamily
880 983 Gene3D G3DSA:3.30.300.30 -
880 983 InterPro IPR045851 AMP-binding enzyme, C-terminal domain superfamily
475 879 FunFam G3DSA:3.40.50.12780:FF:000012 Non-ribosomal peptide synthetase
1683 1694 ProSitePatterns PS00455 Putative AMP-binding domain signature.
1683 1694 InterPro IPR020845 AMP-binding, conserved site
1855 1932 FunFam G3DSA:2.30.38.10:FF:000001 Non-ribosomal peptide synthetase PvdI
1258 1435 FunFam G3DSA:3.30.559.30:FF:000001 Non-ribosomal peptide synthetase
2047 2128 Gene3D G3DSA:1.10.1200.10 -
2047 2128 InterPro IPR036736 ACP-like superfamily
995 1064 SMART SM00823 Phosphopantetheine attachment site
995 1064 InterPro IPR020806 Polyketide synthase, phosphopantetheine-binding domain
2058 2127 SMART SM00823 Phosphopantetheine attachment site
2058 2127 InterPro IPR020806 Polyketide synthase, phosphopantetheine-binding domain
1258 1504 Gene3D G3DSA:3.30.559.30 Nonribosomal peptide synthetase, condensation domain
199 450 SUPERFAMILY SSF52777 CoA-dependent acyltransferases
18 442 CDD cd19531 LCL_NRPS-like
2050 2121 SUPERFAMILY SSF47336 ACP-like
2050 2121 InterPro IPR036736 ACP-like superfamily
623 634 ProSitePatterns PS00455 Putative AMP-binding domain signature.
623 634 InterPro IPR020845 AMP-binding, conserved site
2082 2097 ProSitePatterns PS00012 Phosphopantetheine attachment site.
2082 2097 InterPro IPR006162 Phosphopantetheine attachment site
989 1064 ProSiteProfiles PS50075 Carrier protein (CP) domain profile.
989 1064 InterPro IPR009081 Phosphopantetheine binding ACP domain
20 210 FunFam G3DSA:3.30.559.10:FF:000012 Non-ribosomal peptide synthetase
1081 1270 FunFam G3DSA:3.30.559.10:FF:000012 Non-ribosomal peptide synthetase
1077 1519 Pfam PF00668 Condensation domain
1077 1519 InterPro IPR001242 Condensation domain
16 458 Pfam PF00668 Condensation domain
16 458 InterPro IPR001242 Condensation domain
197 377 FunFam G3DSA:3.30.559.30:FF:000001 Non-ribosomal peptide synthetase
1081 1254 SUPERFAMILY SSF52777 CoA-dependent acyltransferases
19 390 Gene3D G3DSA:3.30.559.10 -
19 390 InterPro IPR023213 Chloramphenicol acetyltransferase-like domain superfamily
1562 1966 NCBIfam TIGR01733 amino acid adenylation domain
1562 1966 InterPro IPR010071 Amino acid adenylation domain
502 909 NCBIfam TIGR01733 amino acid adenylation domain
502 909 InterPro IPR010071 Amino acid adenylation domain
2052 2127 ProSiteProfiles PS50075 Carrier protein (CP) domain profile.
2052 2127 InterPro IPR009081 Phosphopantetheine binding ACP domain
1549 2039 CDD cd17649 A_NRPS_PvdJ-like
1499 2071 SUPERFAMILY SSF56801 Acetyl-CoA synthetase-like
1019 1034 ProSitePatterns PS00012 Phosphopantetheine attachment site.
1019 1034 InterPro IPR006162 Phosphopantetheine attachment site
986 1063 FunFam G3DSA:1.10.1200.10:FF:000005 Nonribosomal peptide synthetase 1
1545 1854 Gene3D G3DSA:3.40.50.980 -
503 638 Gene3D G3DSA:3.40.50.980 -
1563 1698 Gene3D G3DSA:3.40.50.980 -
1080 1450 Gene3D G3DSA:3.30.559.10 -
1080 1450 InterPro IPR023213 Chloramphenicol acetyltransferase-like domain superfamily
226 1352 PANTHER PTHR45527 NONRIBOSOMAL PEPTIDE SYNTHETASE
489 976 CDD cd17649 A_NRPS_PvdJ-like
1936 2046 FunFam G3DSA:3.30.300.30:FF:000010 Enterobactin synthetase component F
988 1060 SUPERFAMILY SSF47336 ACP-like
988 1060 InterPro IPR036736 ACP-like superfamily
1950 2032 Pfam PF13193 AMP-binding enzyme C-terminal domain
1950 2032 InterPro IPR025110 AMP-binding enzyme, C-terminal domain
894 969 Pfam PF13193 AMP-binding enzyme C-terminal domain
894 969 InterPro IPR025110 AMP-binding enzyme, C-terminal domain
20 193 SUPERFAMILY SSF52777 CoA-dependent acyltransferases
1859 1935 Gene3D G3DSA:2.30.38.10 Luciferase; Domain 3
803 879 Gene3D G3DSA:2.30.38.10 Luciferase; Domain 3
984 1065 Gene3D G3DSA:1.10.1200.10 -
984 1065 InterPro IPR036736 ACP-like superfamily
1563 1698 FunFam G3DSA:3.40.50.980:FF:000001 Non-ribosomal peptide synthetase
880 983 FunFam G3DSA:3.30.300.30:FF:000010 Enterobactin synthetase component F
2059 2121 Pfam PF00550 Phosphopantetheine attachment site
2059 2121 InterPro IPR009081 Phosphopantetheine binding ACP domain
997 1058 Pfam PF00550 Phosphopantetheine attachment site
997 1058 InterPro IPR009081 Phosphopantetheine binding ACP domain
503 638 FunFam G3DSA:3.40.50.980:FF:000001 Non-ribosomal peptide synthetase
1260 1504 SUPERFAMILY SSF52777 CoA-dependent acyltransferases

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

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 PA2400
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 0.72
2 0.458
3 0.456

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
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 64 via homologs
Structural ligands 14 0 loaded crystals
Bioactive compounds 0 50 ZINC candidates
Drug-like & clean 26 0 PAINS alerts
Best available ligand signal
5FQ PDB via homolog 158.2 Da · LogP 0.64 · TPSA 55.1
5FQ PDB via homolog 5S4 PDB via homolog 9EF PDB via homolog APC PDB via homolog

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.