Binder profile

GCP

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

Bound to: PA3686 — adenylate kinase

Via homolog PDB 6f7u UniProt P69441 C11H18N5O13P3
Mol. weight 521.21 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GCP
PDB
6f7u
UniProt (similar protein)
P69441
Target protein
PA3686

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 521.21 Da
LogP (Crippen) -2.22
H-bond donors 8
H-bond acceptors 13
TPSA 289.87 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 32
Fraction sp³ C 0.55
Formula C11H18N5O13P3

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 521.2
  • LogP ≤ 5 -2.22
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 289.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(CP(=O)(O)O)O)O)O)N=C(NC2=O)N
InChI 
InChI=1S/C11H18N5O13P3/c12-11-14-8-5(9(19)15-11)13-2-16(8)10-7(18)6(17)4(28-10)1-27-32(25,26)29-31(23,24)3-30(20,21)22/h2,4,6-7,10,17-18H,1,3H2,(H,23,24)(H,25,26)(H2,20,21,22)(H3,12,14,15,19)/t4-,6-,7-,10-/m1/s1
InChIKey 
PHBDHXOBFUBCJD-KQYNXXCUSA-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
PF00406' 'PF05191

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA3686.

PDB 4

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

Ligand PDB entry

ChEMBL 1

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)