Ligand profile

B8C

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

Bound to: KP13_04637 — L-lactate dehydrogenase cytochrome

Via homolog PDB 6a39 UniProt O52792 Formula C₂₁H₂₅N₄O₁₅P
Mol. weight 604.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
B8C
PDB
6a39
UniProt (similar protein)
O52792
Target protein
KP13_04637

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 604.42 Da
LogP (Crippen) -1.97
H-bond donors 10
H-bond acceptors 13
TPSA 305.31 Ų
Rotatable bonds 11
Aromatic rings 1 / 3
Heavy atoms 41
Fraction sp³ C 0.38
Formula C₂₁H₂₅N₄O₁₅P

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 305.3
  • −1 ≤ LogP ≤ 5 -1.97
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 604.4
  • LogP ≤ 5 -1.97
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 305.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)[C@@]3(N2)O/C(=C(\C(=O)O)/O)/C(=O)O)C[C@@H]([C@@H]([C@H](COP(=O)(O)O)O)O)O
InChI 
InChI=1S/C21H25N4O15P/c1-7-3-9-10(4-8(7)2)25(5-11(26)13(28)12(27)6-39-41(36,37)38)18-21(24-9,19(34)23-20(35)22-18)40-15(17(32)33)14(29)16(30)31/h3-4,11-13,24,26-29H,5-6H2,1-2H3,(H,30,31)(H,32,33)(H,23,34,35)(H2,36,37,38)/b15-14+/t11-,12-,13-,21-/m0/s1
InChIKey 
CYUZEIATLQOYCB-IVDAFHBWSA-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
PF01070

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_04637.

PDB 40

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

Ligand PDB entry

ChEMBL 100

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)