Protein profile

KP13_04826

High-molecular-weight protein 2

Genome: KpKP13

Gene: irp2 AHE43793.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H0D3
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Amino acids 2035
Annotations 6
Features 72
PDB binders 15
Druggability 0.976

Overview

Basic information about this protein and its source genome.

Accession
KP13_04826
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
irp2 AHE43793.1
Status
annotated
Amino acids
2035
Structure source
AlphaFold + ColabFold
GO
GO:0031177 Binding to phosphopantetheine, the vitamin pantetheine 4'-(dihydrogen phosphate). 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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0016877 Catalysis of the joining of two molecules via a carbon-sulfur bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate. GO:0043041 Activation of an amino acid for incorporation into a peptide by a nonribosomal process. GO:0009403 The chemical reactions and pathways resulting in the formation of toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
35.443
Human E-value
7.39e-07
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
42.742
DEG E-value
2.95e-17
Localization
CytoplasmicMembrane
ColabFold pLDDT
85.05

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 0.976
Structure A0A0H3H0D3
Pocket Pocket 121
P2Rank 0.986
Structure A0A0H3H0D3
Pocket Pocket 1
ColabFold model
FPocket 0.999 · Pocket 100
P2Rank 0.99 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 4 / 4744 genomes with a hit
Normalized 0.001

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • GO:0031177 Binding to phosphopantetheine, the vitamin pantetheine 4'-(dihydrogen phosphate).
  • 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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0016877 Catalysis of the joining of two molecules via a carbon-sulfur bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
  • GO:0043041 Activation of an amino acid for incorporation into a peptide by a nonribosomal process.
  • GO:0009403 The chemical reactions and pathways resulting in the formation of toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism.

Sequence Features

Domain/signature hits from InterPro and related databases.

72 records
Show feature table
Start End DB Term Name
960 1056 Gene3D G3DSA:3.30.300.30 -
960 1056 InterPro IPR045851 AMP-binding enzyme, C-terminal domain superfamily
1943 2017 ProSiteProfiles PS50075 Carrier protein (CP) domain profile.
1943 2017 InterPro IPR009081 Phosphopantetheine binding ACP domain
1489 1680 SUPERFAMILY SSF52777 CoA-dependent acyltransferases
1946 2014 SUPERFAMILY SSF47336 ACP-like
1946 2014 InterPro IPR036736 ACP-like superfamily
1164 1320 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
1164 1320 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
1398 1480 Gene3D G3DSA:1.10.1200.10 -
1398 1480 InterPro IPR036736 ACP-like superfamily
566 959 FunFam G3DSA:3.40.50.12780:FF:000012 Non-ribosomal peptide synthetase
575 965 Pfam PF00501 AMP-binding enzyme
575 965 InterPro IPR000873 AMP-dependent synthetase/ligase domain
1669 1908 SUPERFAMILY SSF52777 CoA-dependent acyltransferases
580 1063 CDD cd12114 A_NRPS_TlmIV_like
296 536 SUPERFAMILY SSF52777 CoA-dependent acyltransferases
1490 1661 Gene3D G3DSA:3.30.559.10 -
1490 1661 InterPro IPR023213 Chloramphenicol acetyltransferase-like domain superfamily
109 291 Gene3D G3DSA:3.30.559.10 -
109 291 InterPro IPR023213 Chloramphenicol acetyltransferase-like domain superfamily
1307 1397 Gene3D G3DSA:3.30.300.30 -
1307 1397 InterPro IPR045851 AMP-binding enzyme, C-terminal domain superfamily
47 62 ProSitePatterns PS00012 Phosphopantetheine attachment site.
47 62 InterPro IPR006162 Phosphopantetheine attachment site
709 720 ProSitePatterns PS00455 Putative AMP-binding domain signature.
709 720 InterPro IPR020845 AMP-binding, conserved site
594 990 NCBIfam TIGR01733 amino acid adenylation domain
594 990 InterPro IPR010071 Amino acid adenylation domain
568 958 Gene3D G3DSA:3.40.50.12780 -
568 958 InterPro IPR042099 ANL, N-terminal domain
549 1422 SUPERFAMILY SSF56801 Acetyl-CoA synthetase-like
1530 1905 Pfam PF00668 Condensation domain
1530 1905 InterPro IPR001242 Condensation domain
150 535 Pfam PF00668 Condensation domain
150 535 InterPro IPR001242 Condensation domain
1404 1478 ProSiteProfiles PS50075 Carrier protein (CP) domain profile.
1404 1478 InterPro IPR009081 Phosphopantetheine binding ACP domain
15 91 ProSiteProfiles PS50075 Carrier protein (CP) domain profile.
15 91 InterPro IPR009081 Phosphopantetheine binding ACP domain
1148 1306 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
1148 1306 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
1705 1903 PANTHER PTHR45527 NONRIBOSOMAL PEPTIDE SYNTHETASE
1667 1909 FunFam G3DSA:3.30.559.30:FF:000006 Yersiniabactin polyketide/non-ribosomal peptide synthetase
1182 1279 Pfam PF08242 Methyltransferase domain
1182 1279 InterPro IPR013217 Methyltransferase type 12
114 534 CDD cd19535 Cyc_NRPS
1942 2024 Gene3D G3DSA:1.10.1200.10 -
1942 2024 InterPro IPR036736 ACP-like superfamily
1405 1475 SUPERFAMILY SSF47336 ACP-like
1405 1475 InterPro IPR036736 ACP-like superfamily
1952 2013 Pfam PF00550 Phosphopantetheine attachment site
1952 2013 InterPro IPR009081 Phosphopantetheine binding ACP domain
1412 1473 Pfam PF00550 Phosphopantetheine attachment site
1412 1473 InterPro IPR009081 Phosphopantetheine binding ACP domain
22 82 Pfam PF00550 Phosphopantetheine attachment site
22 82 InterPro IPR009081 Phosphopantetheine binding ACP domain
117 289 SUPERFAMILY SSF52777 CoA-dependent acyltransferases
21 124 SUPERFAMILY SSF47336 ACP-like
21 124 InterPro IPR036736 ACP-like superfamily
1410 1478 SMART SM00823 Phosphopantetheine attachment site
1410 1478 InterPro IPR020806 Polyketide synthase, phosphopantetheine-binding domain
1949 2017 SMART SM00823 Phosphopantetheine attachment site
1949 2017 InterPro IPR020806 Polyketide synthase, phosphopantetheine-binding domain
1490 1661 FunFam G3DSA:3.30.559.10:FF:000023 Non-ribosomal peptide synthetase
1495 1906 CDD cd19535 Cyc_NRPS
1180 1282 CDD cd02440 AdoMet_MTases
13 93 Gene3D G3DSA:1.10.1200.10 -
13 93 InterPro IPR036736 ACP-like superfamily
1669 1908 Gene3D G3DSA:3.30.559.30 Nonribosomal peptide synthetase, condensation domain
296 539 Gene3D G3DSA:3.30.559.30 Nonribosomal peptide synthetase, condensation domain
109 287 FunFam G3DSA:3.30.559.10:FF:000023 Non-ribosomal peptide synthetase

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 + 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_A0A0H3H0D3
AlphaFold — — full sequence — Viewing
ColabFold KP13_04826
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
121 0.976
68 0.923
1 0.908
35 0.449

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 43.31 0.97
2 29.43 0.931
3 22.46 0.881
4 12.51 0.653
5 10.61 0.57

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.

66 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)…
AKR
6LTA
A0A077JG85 72.1 Da LogP 0.26 TPSA 37.3 ✓ Ro5 ✓ Clean C=CC(=O)O
ANP
6LTB
A0A077JG85 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
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)…
B6G
5WMM
Q333U7 432.3 Da LogP -1.37 TPSA 218.2 1 viol. ✓ Clean CC(C)[C@@H](C(=O)OP(=O)(O)O[C@H]1[C@H]([C@H]([C…
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
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…
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.