6W7O | pdb_00006w7o

Ternary complex structure - BTK cIAP compound 17

• PDB DOI: https://doi.org/10.2210/pdb6W7O/pdb

• Classification: LIGASE/TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera aff. frugiperda 2 RZ-2014, Escherichia coli
• Mutation(s): No 


• Deposited: 2020-03-19 Released: 2020-11-18 
• Deposition Author(s): Calabrese, M.F., Schiemer, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.240 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Models: experimental

Literature

Structural Characterization of BTK:PROTAC:cIAP Ternary Complexes: From Snapshots to Ensembles

Calabrese, M.F., Schiemer, J.S., Horst, R., Meng, Y., Montgomery, J., Xu, Y., Feng, X., Borzilleri, K., Uccello, D.P., Leverett, C., Brown, S., Che, Y., Brown, M.F., Hayward, M.M., Gilbert, A.M., Noe, M.C.

(2020) Nat Chem Biol 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: cross-linking

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 89.16 kDa 
• Atom Count: 6,242 
• Modeled Residue Count: 709 
• Deposited Residue Count: 752 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase BTK	A, B	277	Homo sapiens	Mutation(s): 0  Gene Names: BTK, AGMX1, ATK, BPK EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q06187 (Homo sapiens) Explore Q06187  Go to UniProtKB:  Q06187
PHAROS:  Q06187 GTEx:  ENSG00000010671

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Baculoviral IAP repeat-containing protein 2	C, D	99	Homo sapiens	Mutation(s): 0  Gene Names: BIRC2, API1, MIHB, RNF48 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q13490 (Homo sapiens) Explore Q13490  Go to UniProtKB:  Q13490
PHAROS:  Q13490 GTEx:  ENSG00000110330

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TL7 (Subject of Investigation/LOI)	E [auth A], F [auth B]	[5-({[(3S)-2-(N-methyl-L-alanyl-3-methyl-L-valyl)-3-{[(1R)-1,2,3,4-tetrahydronaphthalen-1-yl]carbamoyl}-1,2,3,4-tetrahydroisoquinolin-7-yl]oxy}methyl)pyrazin-2-yl]methyl (3R)-3-{5-amino-4-carbamoyl-3-[4-(2,4-difluorophenoxy)phenyl]-1H-pyrazol-1-yl}piperidine-1-carboxylate C58 H65 F2 N11 O8 PTEVOZUKHQQUNI-DLUJOBAXSA-N
ZN	G [auth C], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.240 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.98	α = 104.98
b = 56.33	β = 100.89
c = 98.12	γ = 90.13

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): Calabrese, M.F., Schiemer, J.S.

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description