Ligand profile

NOV

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

Bound to: KP13_00007 — Ribose import ATP-binding protein rbsA

Via homolog PDB 6mit UniProt A0A0H3CR83 Formula C₃₁H₃₆N₂O₁₁
Mol. weight 612.63 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NOV
PDB
6mit
UniProt (similar protein)
A0A0H3CR83
Target protein
KP13_00007

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 612.63 Da
LogP (Crippen) 3.63
H-bond donors 5
H-bond acceptors 11
TPSA 200.01 Ų
Rotatable bonds 8
Aromatic rings 3 / 4
Heavy atoms 44
Fraction sp³ C 0.39
Formula C₃₁H₃₆N₂O₁₁

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 200.0
  • −1 ≤ LogP ≤ 5 3.63
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 612.6
  • LogP ≤ 5 3.63
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 200.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(ccc2c1OC(=O)C(=C2O)NC(=O)c3ccc(c(c3)CC=C(C)C)O)O[C@H]4[C@@H]([C@@H]([C@H](C(O4)(C)C)OC)OC(=O)N)O
InChI 
InChI=1S/C31H36N2O11/c1-14(2)7-8-16-13-17(9-11-19(16)34)27(37)33-21-22(35)18-10-12-20(15(3)24(18)42-28(21)38)41-29-23(36)25(43-30(32)39)26(40-6)31(4,5)44-29/h7,9-13,23,25-26,29,34-36H,8H2,1-6H3,(H2,32,39)(H,33,37)/t23-,25+,26-,29-/m1/s1
InChIKey 
YJQPYGGHQPGBLI-KGSXXDOSSA-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
PF00005

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_00007.

PDB 12

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)