Ligand profile

B13

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

Bound to: KP13_00354 — Methionine synthase

Via homolog PDB 2i2x UniProt Q46EH4 Formula C₆₀H₈₈CoN₁₃O₁₅P
Mol. weight 1321.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
B13
PDB
2i2x
UniProt (similar protein)
Q46EH4
Target protein
KP13_00354

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 1321.35 Da
LogP (Crippen) 1.51
H-bond donors 11
H-bond acceptors 20
TPSA 444.10 Ų
Rotatable bonds 26
Aromatic rings 2 / 11
Heavy atoms 90
Fraction sp³ C 0.67
Formula C₆₀H₈₈CoN₁₃O₁₅P

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 444.1
  • −1 ≤ LogP ≤ 5 1.51
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 1321.3
  • LogP ≤ 5 1.51
  • H-bond donors ≤ 5 11
  • H-bond acceptors ≤ 10 20
Veber's rules Fail
  • Rotatable bonds ≤ 10 26
  • TPSA ≤ 140 Ų 444.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1=C2[C@@]([C@@H](C3=CC4C([C@@H](C5=C(C6[C@]([C@H]([C@H]7N6[Co](N45)(N32)N8C1[C@H]([C@]([C@]78C)(C)CC(=O)N)CCC(=O)N)CC(=O)N)(C)CCC(=O)NC[C@@H](C)O[P@@](=O)(O)O[C@@H]9[C@H](O[C@@H]([C@@H]9O)n1cnc2c1ccc(c2)O)CO)C)CCC(=O)N)(C)C)CCC(=O)N)(C)CC(=O)N
InChI 
InChI=1S/C60H88N13O15P.Co/c1-28(87-89(84,85)88-51-39(26-74)86-55(50(51)83)73-27-68-37-20-31(75)10-14-38(37)73)25-67-47(82)18-19-57(6)35(21-44(64)79)54-60(9)59(8,24-46(66)81)34(13-17-43(63)78)49(72-60)30(3)53-58(7,23-45(65)80)32(11-15-41(61)76)36(69-53)22-40-56(4,5)33(12-16-42(62)77)48(70-40)29(2)52(57)71-54;/h10,14,20,22,27-28,32-35,39-40,49-52,54-55,74-75,83H,11-13,15-19,21,23-26H2,1-9H3,(H2,61,76)(H2,62,77)(H2,63,78)(H2,64,79)(H2,65,80)(H2,66,81)(H,67,82)(H,84,85);/q-4;+4/t28-,32-,33-,34-,35+,39-,40?,49?,50-,51-,52?,54-,55+,57-,58+,59+,60+;/m1./s1
InChIKey 
QJVWXASLTDBQFK-ORCPYQQTSA-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
PF02310' 'PF12176

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_00354.

PDB 7

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)