Ligand profile

SIR

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

Bound to: KP13_02334 — Sirohydrochlorin cobaltochelatase

Via homolog PDB 2xwp UniProt Q05592 Formula C₄₂H₄₄CoN₄O₁₆⁴⁺
Mol. weight 919.76 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SIR
PDB
2xwp
UniProt (similar protein)
Q05592
Target protein
KP13_02334

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 919.76 Da
LogP (Crippen) 0.84
H-bond donors 8
H-bond acceptors 10
TPSA 314.28 Ų
Rotatable bonds 20
Aromatic rings 2 / 8
Heavy atoms 63
Fraction sp³ C 0.43
Formula C₄₂H₄₄CoN₄O₁₆⁴⁺

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 314.3
  • −1 ≤ LogP ≤ 5 0.84
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 919.8
  • LogP ≤ 5 0.84
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 20
  • TPSA ≤ 140 Ų 314.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@]1(c2cc3c(c(c4n3[Co+2]56[n+]2c(cc7[n+]5c(cc8n6c(c4)c(c8CC(=O)O)CCC(=O)O)[C@H]([C@]7(C)CC(=O)O)CCC(=O)O)[C@H]1CCC(=O)O)CCC(=O)O)CC(=O)O)CC(=O)O
InChI 
InChI=1S/C42H46N4O16.Co/c1-41(17-39(59)60)23(5-9-35(51)52)29-14-27-21(11-37(55)56)19(3-7-33(47)48)25(43-27)13-26-20(4-8-34(49)50)22(12-38(57)58)28(44-26)15-31-42(2,18-40(61)62)24(6-10-36(53)54)30(46-31)16-32(41)45-29;/h13-16,23-24H,3-12,17-18H2,1-2H3,(H10,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62);/q;+6/p-2/t23-,24-,41+,42+;/m1./s1
InChIKey 
OLKORPGWPQXDAV-QIISWYHFSA-L

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
PF06180

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_02334.

PDB 2

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

Ligand PDB entry