Ligand profile

K5K

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

Bound to: KP13_02169 — D-3-phosphoglycerate dehydrogenase

Via homolog PDB 6rj6 UniProt O43175 Formula C₂₁H₂₀Cl₂N₂O₆S
Mol. weight 499.37 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
K5K
PDB
6rj6
UniProt (similar protein)
O43175
Target protein
KP13_02169

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 499.37 Da
LogP (Crippen) 3.12
H-bond donors 3
H-bond acceptors 6
TPSA 125.70 Ų
Rotatable bonds 7
Aromatic rings 3 / 3
Heavy atoms 32
Fraction sp³ C 0.24
Formula C₂₁H₂₀Cl₂N₂O₆S

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 125.7
  • −1 ≤ LogP ≤ 5 3.12
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 499.4
  • LogP ≤ 5 3.12
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 125.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc2c(cc(n2C)C(=O)N[C@H](CO)c3ccc(cc3)S(=O)(=O)CC(=O)O)c(c1Cl)Cl
InChI 
InChI=1S/C21H20Cl2N2O6S/c1-11-7-16-14(20(23)19(11)22)8-17(25(16)2)21(29)24-15(9-26)12-3-5-13(6-4-12)32(30,31)10-18(27)28/h3-8,15,26H,9-10H2,1-2H3,(H,24,29)(H,27,28)/t15-/m1/s1
InChIKey 
CJEJFFCPVBZSIE-OAHLLOKOSA-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
PF02826

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_02169.

PDB 19

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)