Ligand profile

6V0

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

Bound to: KP13_02981 — Malate dehydrogenase

Via homolog PDB 5kka UniProt P61889 Formula C₂₁H₂₉N₇O₁₄P₂
Mol. weight 665.45 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6V0
PDB
5kka
UniProt (similar protein)
P61889
Target protein
KP13_02981

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 665.45 Da
LogP (Crippen) -3.03
H-bond donors 8
H-bond acceptors 18
TPSA 317.62 Ų
Rotatable bonds 11
Aromatic rings 2 / 5
Heavy atoms 44
Fraction sp³ C 0.52
Formula C₂₁H₂₉N₇O₁₄P₂

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 317.6
  • −1 ≤ LogP ≤ 5 -3.03
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 665.4
  • LogP ≤ 5 -3.03
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 18
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 317.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5CC=CC(=C5)C(=O)N)O)O)O)O)N
InChI 
InChI=1S/C21H29N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-2,4,7-8,10-11,13-16,20-21,29-32H,3,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKey 
QVQHBKNZCMZBKP-NNYOXOHSSA-N

Provenance

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

Method
LigQ sequence
Source
PDB
Binding sites
PF00056' 'PF02866

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_02981.

PDB 3

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)