Ligand profile

1HA

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

Bound to: VK055_4855 — naphthoate synthase

Via homolog PDB 4i42 UniProt P0ABU0 Formula C₃₂H₄₂N₇O₁₈P₃S
Mol. weight 937.71 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1HA
PDB
4i42
UniProt (similar protein)
P0ABU0
Target protein
VK055_4855

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 937.71 Da
LogP (Crippen) 0.84
H-bond donors 10
H-bond acceptors 20
TPSA 383.86 Ų
Rotatable bonds 20
Aromatic rings 4 / 5
Heavy atoms 61
Fraction sp³ C 0.44
Formula C₃₂H₄₂N₇O₁₈P₃S

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 383.9
  • −1 ≤ LogP ≤ 5 0.84
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 937.7
  • LogP ≤ 5 0.84
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 20
Veber's rules Fail
  • Rotatable bonds ≤ 10 20
  • TPSA ≤ 140 Ų 383.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCSC(=O)c4ccc5ccccc5c4O)O
InChI 
InChI=1S/C32H42N7O18P3S/c1-32(2,26(43)29(44)35-10-9-21(40)34-11-12-61-31(45)19-8-7-17-5-3-4-6-18(17)23(19)41)14-54-60(51,52)57-59(49,50)53-13-20-25(56-58(46,47)48)24(42)30(55-20)39-16-38-22-27(33)36-15-37-28(22)39/h3-8,15-16,20,24-26,30,41-43H,9-14H2,1-2H3,(H,34,40)(H,35,44)(H,49,50)(H,51,52)(H2,33,36,37)(H2,46,47,48)/t20-,24-,25-,26+,30-/m1/s1
InChIKey 
ZHSLHXZSNOSMQG-HSJNEKGZSA-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
PF00378

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to VK055_4855.

PDB 11

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

Ligand PDB entry

ChEMBL 10

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)