Ligand profile

CZD

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

Bound to: KP13_00812 — Signal peptidase I

Via homolog PDB 6b88 UniProt P00803 Formula C₄₇H₆₁N₁₁O₇
Mol. weight 892.07 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CZD
PDB
6b88
UniProt (similar protein)
P00803
Target protein
KP13_00812

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 892.07 Da
LogP (Crippen) 2.05
H-bond donors 8
H-bond acceptors 13
TPSA 282.86 Ų
Rotatable bonds 16
Aromatic rings 4 / 5
Heavy atoms 65
Fraction sp³ C 0.40
Formula C₄₇H₆₁N₁₁O₇

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 282.9
  • −1 ≤ LogP ≤ 5 2.05
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 892.1
  • LogP ≤ 5 2.05
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 16
  • TPSA ≤ 140 Ų 282.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[H]/N=C\CNC(=O)[C@@H]1Cc2ccc(c(c2)-c3cc(ccc3OCCN)[C@@H](C(=O)N[C@H](C(=O)N1)C)N(C)C(=O)[C@H](CCN)NC(=O)c4cnc(nc4C)c5ccc(cc5)C(C)(C)C)OCCN
InChI 
InChI=1S/C47H61N11O7/c1-27-35(26-53-41(54-27)30-8-11-32(12-9-30)47(3,4)5)43(60)56-36(15-16-48)46(63)58(6)40-31-10-14-39(65-22-19-51)34(25-31)33-23-29(7-13-38(33)64-21-18-50)24-37(44(61)52-20-17-49)57-42(59)28(2)55-45(40)62/h7-14,17,23,25-26,28,36-37,40,49H,15-16,18-22,24,48,50-51H2,1-6H3,(H,52,61)(H,55,62)(H,56,60)(H,57,59)/b49-17-/t28-,36-,37-,40-/m0/s1
InChIKey 
SJYWASAPFZIDQL-UAKBWTGGSA-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
PF10502

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_00812.

ChEMBL 28

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)