Ligand profile

7DT

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

Bound to: KP13_01981 — Chaperone protein dnaK

Via homolog PDB 5exw UniProt P11021 Formula C₁₁H₁₇N₄O₁₃P₃
Mol. weight 506.19 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
7DT
PDB
5exw
UniProt (similar protein)
P11021
Target protein
KP13_01981

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 506.19 Da
LogP (Crippen) -1.02
H-bond donors 7
H-bond acceptors 13
TPSA 266.24 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 31
Fraction sp³ C 0.45
Formula C₁₁H₁₇N₄O₁₃P₃

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 266.2
  • −1 ≤ LogP ≤ 5 -1.02
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 506.2
  • LogP ≤ 5 -1.02
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 266.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cn(c2c1c(ncn2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
InChI 
InChI=1S/C11H17N4O13P3/c12-9-5-1-2-15(10(5)14-4-13-9)11-8(17)7(16)6(26-11)3-25-30(21,22)28-31(23,24)27-29(18,19)20/h1-2,4,6-8,11,16-17H,3H2,(H,21,22)(H,23,24)(H2,12,13,14)(H2,18,19,20)/t6-,7-,8-,11-/m1/s1
InChIKey 
GVVRDIINMFAFEO-KCGFPETGSA-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
PF00012

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_01981.

PDB 19

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

Ligand PDB entry

ChEMBL 100

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)