Binder profile

2MD

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

Bound to: PA2714 — molybdopterin oxidoreductase

Via homolog PDB 2iv2 UniProt P07658 C20H28N10O13P2S2
Mol. weight 742.58 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2MD
PDB
2iv2
UniProt (similar protein)
P07658
Target protein
PA2714

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 742.58 Da
LogP (Crippen) -2.53
H-bond donors 12
H-bond acceptors 21
TPSA 346.63 Ų
Rotatable bonds 9
Aromatic rings 3 / 6
Heavy atoms 47
Fraction sp³ C 0.55
Formula C20H28N10O13P2S2

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 742.6
  • LogP ≤ 5 -2.53
  • H-bond donors ≤ 5 12
  • H-bond acceptors ≤ 10 21
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 346.6
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)(O)OC[C@@H]4[C@@H]([C@@H]([C@H]5[C@@H](O4)NC6=C(N5)C(=O)NC(=N6)N)S)S)O)O)N=C(NC2=O)N
InChI 
InChI=1S/C20H28N10O13P2S2/c21-19-26-13-7(15(33)28-19)24-6-12(47)11(46)5(41-17(6)25-13)2-40-45(37,38)43-44(35,36)39-1-4-9(31)10(32)18(42-4)30-3-23-8-14(30)27-20(22)29-16(8)34/h3-6,9-12,17-18,24,31-32,46-47H,1-2H2,(H,35,36)(H,37,38)(H3,22,27,29,34)(H4,21,25,26,28,33)/t4-,5-,6+,9-,10-,11+,12-,17-,18-/m1/s1
InChIKey 
YDYCAANTTOPADF-JKOCJXFLSA-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
PF00384' 'PF01568

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA2714.

PDB 8

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)