Ligand profile

3TT

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

Bound to: KP13_32224 — DNA polymerase IV

Via homolog PDB 4qwd UniProt Q97W02 Formula C₈H₁₅N₄O₁₁P₃S
Mol. weight 468.21 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3TT
PDB
4qwd
UniProt (similar protein)
Q97W02
Target protein
KP13_32224

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 468.21 Da
LogP (Crippen) -0.67
H-bond donors 6
H-bond acceptors 11
TPSA 232.76 Ų
Rotatable bonds 8
Aromatic rings 1 / 2
Heavy atoms 27
Fraction sp³ C 0.50
Formula C₈H₁₅N₄O₁₁P₃S

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 232.8
  • −1 ≤ LogP ≤ 5 -0.67
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 468.2
  • LogP ≤ 5 -0.67
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 232.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@H](O[C@H](S1)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)N2C=CC(=NC2=O)N
InChI 
InChI=1S/C8H15N4O11P3S/c9-5-1-2-12(8(13)10-5)6-4-27-7(22-6)3-21-26(19,20)23-25(17,18)11-24(14,15)16/h1-2,6-7H,3-4H2,(H,19,20)(H2,9,10,13)(H4,11,14,15,16,17,18)/t6-,7+/m0/s1
InChIKey 
KGYPGPIERPVYLF-NKWVEPMBSA-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
PF00817

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_32224.

PDB 31

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

Ligand PDB entry

ChEMBL 3

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)