Binder profile

CZD

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

Bound to: PA1303 — signal peptidase

Via homolog PDB 6b88 UniProt P00803 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
PA1303

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.

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 TPW step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF10502

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other binders for this protein

Quick navigation to other ligands bound to PA1303.

PDB 1

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

Ligand PDB entry

ChEMBL 28

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)