Ligand profile

9PX

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

Bound to: KP13_04637 — L-lactate dehydrogenase cytochrome

Via homolog PDB 6a3d UniProt O52792 Formula C₁₉H₂₅N₄O₁₃P
Mol. weight 548.40 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9PX
PDB
6a3d
UniProt (similar protein)
O52792
Target protein
KP13_04637

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 548.40 Da
LogP (Crippen) -1.21
H-bond donors 7
H-bond acceptors 13
TPSA 246.01 Ų
Rotatable bonds 9
Aromatic rings 1 / 3
Heavy atoms 37
Fraction sp³ C 0.47
Formula C₁₉H₂₅N₄O₁₃P

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 246.0
  • −1 ≤ LogP ≤ 5 -1.21
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 548.4
  • LogP ≤ 5 -1.21
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 246.0
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)OOC(=O)OC)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O
InChI 
InChI=1S/C19H25N4O13P/c1-8-4-10-11(5-9(8)2)23(6-12(24)14(26)13(25)7-34-37(30,31)32)15-19(22-10,36-35-18(29)33-3)16(27)21-17(28)20-15/h4-5,12-14,22,24-26H,6-7H2,1-3H3,(H,21,27,28)(H2,30,31,32)/t12-,13+,14-,19-/m0/s1
InChIKey 
BKTAMFVARSDVLC-LJPSSGMGSA-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)