Protein profile

KP13_02514

2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

Genome: KpKP13

Gene: ispD AHE42980.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GWT7
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Amino acids 236
Annotations 6
Features 21
PDB binders 7
Druggability 0.114

Overview

Basic information about this protein and its source genome.

Accession
KP13_02514
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
ispD AHE42980.1
Status
annotated
Amino acids
236
Structure source
AlphaFold + ColabFold
EC
2.7.7.60
GO
GO:0008299 The chemical reactions and pathways resulting in the formation of an isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues. 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:0070567 Catalysis of the transfer of a cytidylyl group to an acceptor. GO:0050518 Catalysis of the reaction: 2-C-methyl-D-erythritol 4-phosphate + CTP = 4-CDP-2-C-methyl-D-erythritol + diphosphate. GO:0019288 The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
26.984
Human E-value
3.14e-16
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
86.864
DEG E-value
3.33e-152
Localization
Cytoplasmic
ColabFold pLDDT
93.17

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 0.114
Structure A0A0H3GWT7
Pocket Pocket 12
P2Rank 0.37
Structure A0A0H3GWT7
Pocket Pocket 1
ColabFold model
FPocket 0.377 · Pocket 5
P2Rank 0.363 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 144 / 4744 genomes with a hit
Normalized 0.03

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0008299 The chemical reactions and pathways resulting in the formation of an isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
  • 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:0070567 Catalysis of the transfer of a cytidylyl group to an acceptor.
  • GO:0050518 Catalysis of the reaction: 2-C-methyl-D-erythritol 4-phosphate + CTP = 4-CDP-2-C-methyl-D-erythritol + diphosphate.
  • GO:0019288 The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
4 235 Gene3D G3DSA:3.90.550.10 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
4 235 InterPro IPR029044 Nucleotide-diphospho-sugar transferases
7 227 Hamap MF_00108 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase [ispD].
7 227 InterPro IPR001228 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
8 233 PANTHER PTHR32125 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, CHLOROPLASTIC
8 229 Pfam PF01128 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
8 229 InterPro IPR034683 Cytidylyltransferase IspD/TarI
15 236 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
9 227 NCBIfam TIGR00453 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
9 227 InterPro IPR001228 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
102 109 ProSitePatterns PS01295 4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature.
102 109 InterPro IPR018294 4-diphosphocytidyl-2C-methyl-D-erythritol synthase, conserved site
10 14 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
8 227 SUPERFAMILY SSF53448 Nucleotide-diphospho-sugar transferases
8 227 InterPro IPR029044 Nucleotide-diphospho-sugar transferases
8 223 CDD cd02516 CDP-ME_synthetase
8 223 InterPro IPR034683 Cytidylyltransferase IspD/TarI
1 14 Phobius SIGNAL_PEPTIDE Signal peptide region
3 232 FunFam G3DSA:3.90.550.10:FF:000003 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
1 1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
2 9 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.

3D Structure

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

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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_A0A0H3GWT7
AlphaFold — — full sequence — Viewing
ColabFold KP13_02514
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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 5.26 0.246
2 1.66 0.028
3 1.42 0.018

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.

63 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
30A
2YCM
P69834 303.7 Da LogP 2.38 TPSA 87.7 ✓ Ro5 ✓ Clean c1ccc(cc1)Cc2c(nc3c(cnn3c2O)C(=O)O)Cl
CAD
4ZDQ
Q2SWT6 138.0 Da LogP 0.11 TPSA 37.3 ✓ Ro5 ✓ Clean C[As](=O)(C)O
CDM
3Q80
P9WKG9 521.3 Da LogP -3.20 TPSA 273.6 3 viol. ✓ Clean C[C@](CO)([C@@H](CO[P@](=O)(O)O[P@](=O)(O)OC[C@…
DTT
4NAL
P69834 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
H70
4NAL
P69834 464.8 Da LogP 5.98 TPSA 36.0 1 viol. ✓ Clean c1c(cc(c(c1c2c(c(c([nH]2)Br)Br)Br)O)Cl)Cl
MW5
2YC3
P69834 260.7 Da LogP 1.66 TPSA 63.1 ✓ Ro5 ✓ Clean c1ccc(cc1)CC2=C(N=C3NC=NN3C2=O)Cl
V2V
6XHQ
Q2G1C0 537.3 Da LogP -4.23 TPSA 293.8 3 viol. ✓ Clean C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H](C(O2)COP(=…

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.