Ligand profile

RAP

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

Bound to: VK055_2441 — FKBP-type peptidyl-prolyl cis-trans isomerase family protein

Via homolog PDB 2vcd UniProt Q5ZXE0 Formula C₅₁H₇₉NO₁₃
Mol. weight 914.19 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RAP
PDB
2vcd
UniProt (similar protein)
Q5ZXE0
Target protein
VK055_2441

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 914.19 Da
LogP (Crippen) 6.18
H-bond donors 3
H-bond acceptors 13
TPSA 195.43 Ų
Rotatable bonds 6
Aromatic rings 0 / 4
Heavy atoms 65
Fraction sp³ C 0.75
Formula C₅₁H₇₉NO₁₃

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 195.4
  • −1 ≤ LogP ≤ 5 6.18
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 914.2
  • LogP ≤ 5 6.18
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 195.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1CC[C@H]2C[C@@H](C(=CC=C\C=C\[C@H](C[C@H](C(=O)[C@@H]([C@@H](/C(=C/[C@H](C(=O)C[C@H](OC(=O)[C@@H]3CCCCN3C(=O)C(=O)[C@@]1(O2)O)[C@H](C)C[C@@H]4CC[C@H]([C@@H](C4)OC)O)C)/C)O)OC)C)C)C)OC
InChI 
InChI=1S/C51H79NO13/c1-30-16-12-11-13-17-31(2)42(61-8)28-38-21-19-36(7)51(60,65-38)48(57)49(58)52-23-15-14-18-39(52)50(59)64-43(33(4)26-37-20-22-40(53)44(27-37)62-9)29-41(54)32(3)25-35(6)46(56)47(63-10)45(55)34(5)24-30/h11-13,16-17,25,30,32-34,36-40,42-44,46-47,53,56,60H,14-15,18-24,26-29H2,1-10H3/b13-11?,16-12+,31-17?,35-25+/t30-,32-,33-,34-,36-,37+,38+,39+,40-,42+,43+,44-,46-,47+,51-/m1/s1
InChIKey 
QFJCIRLUMZQUOT-LAOSHSCVSA-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
PF00254

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to VK055_2441.

PDB 1

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 32

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)