Crystal structure of the cytoplasmic domain of the bone morphogenetic protein receptor type-1B (BMPR1B) in complex with FKBP12 and LDN-193189

Structural Biology Knowledgebase: 3MDY SBKB.org

Experimental Data Snapshot

  • Resolution: 2.05 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.201

wwPDB Validation Full Report


Sequence Display for 3MDY

Classification: Transferase / isomerase

Total Structure Weight: 101553.48

Macromolecule Entities
Molecule Chains Length Organism Details
Bone morphogenetic protein receptor type-1B A, C 337 Homo sapiens EC#: IUBMB
Fragment: BMPR1B cytoplasmic (GS and kinase) domain (residue 168-502)
Gene Name(s): BMPR1B Gene View
Peptidyl-prolyl cis-trans isomerase FKBP1A B, D 109 Homo sapiens EC#: IUBMB
Fragment: FKBP12
Gene Name(s): FKBP1A Gene View FKBP1 FKBP12

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
Query on LDN

A, C 4-[6-(4-piperazin-1-ylphenyl)pyrazolo[1,5- a]pyrimidin-3-yl]quinoline
C25 H22 N6
Ligand Explorer
Binding Pocket (JSmol)
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
LDN IC50: 14.3 - 60 nM (85 - 100) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Resolution: 2.05 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.201
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 65.41 α = 90.00
b = 80.01 β = 90.00
c = 183.33 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

  • Deposited Date: 2010-03-31
  • Released Date: 2010-05-19
  • Deposition author(s): Chaikuad, A., Sanvitale, C., Mahajan, P., Daga, N., Cooper, C., Krojer, T., Alfano, I., Knapp, S., von Delft, F., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A., Structural Genomics Consortium (SGC)

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4