Ligand profile

V2V

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: KP13_02514 — 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

Via homolog PDB 6xhq UniProt Q2G1C0 Formula C₁₄H₂₅N₃O₁₅P₂
Mol. weight 537.31 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
V2V
PDB
6xhq
UniProt (similar protein)
Q2G1C0
Target protein
KP13_02514

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 537.31 Da
LogP (Crippen) -4.23
H-bond donors 9
H-bond acceptors 16
TPSA 293.81 Ų
Rotatable bonds 12
Aromatic rings 1 / 2
Heavy atoms 34
Fraction sp³ C 0.71
Formula C₁₄H₂₅N₃O₁₅P₂

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 293.8
  • −1 ≤ LogP ≤ 5 -4.23
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 537.3
  • LogP ≤ 5 -4.23
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 16
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 293.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H](C(O2)COP(=O)(O)OP(=O)(O)OC[C@H]([C@H]([C@H](CO)O)O)O)O)O
InChI 
InChI=1S/C14H25N3O15P2/c15-9-1-2-17(14(24)16-9)13-12(23)11(22)8(31-13)5-30-34(27,28)32-33(25,26)29-4-7(20)10(21)6(19)3-18/h1-2,6-8,10-13,18-23H,3-5H2,(H,25,26)(H,27,28)(H2,15,16,24)/t6-,7+,8?,10-,11+,12+,13+/m0/s1
InChIKey 
DPJKHFICSGCNIR-OXLWAXCESA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF01128

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_02514.

PDB 6

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 6

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)