Ligand profile

MRT

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

Bound to: KP13_00958 — Ribonucleoside-diphosphate reductase 1 subunit alpha

Via homolog PDB 2zlg UniProt P21524 Formula C₅₆H₆₆N₆O₁₃
Mol. weight 1031.17 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
MRT
PDB
2zlg
UniProt (similar protein)
P21524
Target protein
KP13_00958

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 1031.17 Da
LogP (Crippen) 4.98
H-bond donors 8
H-bond acceptors 11
TPSA 286.94 Ų
Rotatable bonds 26
Aromatic rings 4 / 6
Heavy atoms 75
Fraction sp³ C 0.41
Formula C₅₆H₆₆N₆O₁₃

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 286.9
  • −1 ≤ LogP ≤ 5 4.98
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 1031.2
  • LogP ≤ 5 4.98
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 26
  • TPSA ≤ 140 Ų 286.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)C[C@@H](C(=O)N[C@@H](CC(=O)O)C(=O)N[C@@H](C1CCCCC1)C(=O)N[C@@H](CC(=O)O)C(=O)N[C@@H](Cc2ccccc2)C(=O)O)NCC(=O)[C@@H](c3ccccc3)N(C)C(=O)OCC4c5ccccc5-c6c4cccc6
InChI 
InChI=1S/C56H66N6O13/c1-33(2)27-42(57-31-46(63)50(36-21-11-6-12-22-36)62(3)56(74)75-32-41-39-25-15-13-23-37(39)38-24-14-16-26-40(38)41)51(68)58-44(30-48(66)67)53(70)61-49(35-19-9-5-10-20-35)54(71)59-43(29-47(64)65)52(69)60-45(55(72)73)28-34-17-7-4-8-18-34/h4,6-8,11-18,21-26,33,35,41-45,49-50,57H,5,9-10,19-20,27-32H2,1-3H3,(H,58,68)(H,59,71)(H,60,69)(H,61,70)(H,64,65)(H,66,67)(H,72,73)/t42-,43-,44-,45-,49-,50+/m0/s1
InChIKey 
VHDDRUTXAIHKQU-NXKHAHLZSA-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
PF02867

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_00958.

PDB 15

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

Ligand PDB entry

ChEMBL 9

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)