6W74 | pdb_00006w74

Structure of cIAP with compound 15

PDB DOI: https://doi.org/10.2210/pdb6W74/pdb

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free:
0.258 (Depositor), 0.256 (DCC)
R-Value Work:
0.187 (Depositor), 0.191 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 12.56 kDa
Atom Count: 775
Modeled Residue Count: 87
Deposited Residue Count: 99
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Baculoviral IAP repeat-containing protein 2	A	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13490
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TKY (Subject of Investigation/LOI) Query on TKY Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	14-{[(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}-3,6,9,12-tetraoxatetradecan-1-yl (3R)-3-{5-amino-4-carbamoyl-3-[4-(2,4-difluorophenoxy)phenyl]-1H-pyrazol-1-yl}piperidine-1-carboxylate C₆₂ H₇₉ F₂ N₉ O₁₂ ZYNKGHHFEDYPKB-HQBWEIPVSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.258 (Depositor), 0.256 (DCC)
R-Value Work: 0.187 (Depositor), 0.191 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.037	α = 90
b = 33.651	β = 105.7
c = 57.61	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-11-18

Deposition Author(s):

Calabrese, M.F.

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.