Ligand profile

5NG

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

Bound to: KP13_00654 — putative N-acetyltransferase

Via homolog PDB 6c37 UniProt A0R3G9 Formula C₄₂H₇₀N₁₄O₃₂P₆S₂
Mol. weight 1533.07 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5NG
PDB
6c37
UniProt (similar protein)
A0R3G9
Target protein
KP13_00654

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 1533.07 Da
LogP (Crippen) -2.80
H-bond donors 18
H-bond acceptors 36
TPSA 693.12 Ų
Rotatable bonds 39
Aromatic rings 4 / 6
Heavy atoms 96
Fraction sp³ C 0.67
Formula C₄₂H₇₀N₁₄O₃₂P₆S₂

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 693.1
  • −1 ≤ LogP ≤ 5 -2.80
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 1533.1
  • LogP ≤ 5 -2.80
  • H-bond donors ≤ 5 18
  • H-bond acceptors ≤ 10 36
Veber's rules Fail
  • Rotatable bonds ≤ 10 39
  • TPSA ≤ 140 Ų 693.1
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)NCCSSCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)OP(=O)(O)O)O)O
InChI 
InChI=1S/C42H70N14O32P6S2/c1-41(2,15-81-93(75,76)87-91(71,72)79-13-21-29(85-89(65,66)67)27(59)39(83-21)55-19-53-25-33(43)49-17-51-35(25)55)31(61)37(63)47-7-5-23(57)45-9-11-95-96-12-10-46-24(58)6-8-48-38(64)32(62)42(3,4)16-82-94(77,78)88-92(73,74)80-14-22-30(86-90(68,69)70)28(60)40(84-22)56-20-54-26-34(44)50-18-52-36(26)56/h17-22,27-32,39-40,59-62H,5-16H2,1-4H3,(H,45,57)(H,46,58)(H,47,63)(H,48,64)(H,71,72)(H,73,74)(H,75,76)(H,77,78)(H2,43,49,51)(H2,44,50,52)(H2,65,66,67)(H2,68,69,70)/t21-,22+,27-,28-,29-,30-,31+,32+,39-,40-/m1/s1
InChIKey 
YAISMNQCMHVVLO-RYNPGVCASA-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
PF13302

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_00654.

PDB 5

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)