36XC | pdb_000036xc

NNVL bound to inhibitor compound 112 (YT-IV-239B)

PDB DOI: https://doi.org/10.2210/pdb36XC/pdb
EM Map EMD-77939: EMDB EMDataResource

Classification: TRANSLOCASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2026-07-05 Released: 2026-11-11
Deposition Author(s): Erzberger, J.P., Cruz, V.E.
Funding Organization(s): Cancer Prevention and Research Institute of Texas (CPRIT), Robert A. Welch Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.59 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Discovery and Optimization of Anticancer Dibenzothiazepinones That Target the Ribosome Biogenesis Factor NVL

Tao, Y., Guo, H.H., Cruz, V.E., Reddy, D., Leach, A., Williams, N.S., Aurora, A.B., Khivansara, V., Han, Y., Erzberger, J.P., Nijhawan, D., De Brabander, J.K.

(2026) J Med Chem

DOI: https://doi.org/10.1021/acs.jmedchem.6c02184

Macromolecule Content

Total Structure Weight: 480.43 kDa
Atom Count: 23,360
Modeled Residue Count: 2,983
Deposited Residue Count: 4,308
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-like domain-containing protein,Nuclear valosin-containing protein-like	A B C E [auth D] F [auth E] A, B, C, E [auth D], F [auth E], G [auth F]	714	Homo sapiens	Mutation(s): 0 Gene Names: OPV22_014368, NVL, NVL2
UniProt & NIH Common Fund Data Resources
Find proteins for A0AAV8R7V6 (Ensete ventricosum) Explore A0AAV8R7V6 Go to UniProtKB: A0AAV8R7V6
Find proteins for O15381 (Homo sapiens) Explore O15381 Go to UniProtKB: O15381
PHAROS: O15381 GTEx: ENSG00000143748
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	A0AAV8R7V6 O15381
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ply-histidine substrate mimic	D [auth G]	24	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth E] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth E] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain X [auth E]	J [auth A] K [auth A] N [auth B] O [auth B] R [auth C] J [auth A], K [auth A], N [auth B], O [auth B], R [auth C], S [auth C], V [auth D], W [auth D], X [auth E]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth E] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth E]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain Y [auth E] MOL2 format, chain Y [auth E] mmCIF format, chain Y [auth E]	Y [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain Y [auth E] Interactions & Density Focus chain Y [auth E]
A1DMC (Subject of Investigation/LOI) Query on A1DMC Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] MOL2 format, chain Z [auth E] mmCIF format, chain Z [auth E]	Z [auth E]	N-[(11S)-5-(but-2-yn-1-yl)-11-methyl-6-oxo-6,11-dihydro-5H-dibenzo[b,e]azepin-2-yl]-4-methoxybenzamide C₂₇ H₂₄ N₂ O₃ UOPYPQPUAYFZKT-SFHVURJKSA-N		Interactions Focus chain Z [auth E] Interactions & Density Focus chain Z [auth E]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain Q [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain Q [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain Q [auth C]	H [auth A] I [auth A] L [auth B] M [auth B] P [auth C] H [auth A], I [auth A], L [auth B], M [auth B], P [auth C], Q [auth C], T [auth D], U [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.59 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-11

Deposition Author(s):

Erzberger, J.P.

Cruz, V.E.

Funding Organization	Location	Grant Number
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RP240320
Robert A. Welch Foundation	United States	I-1422
Robert A. Welch Foundation	United States	I-1879
Robert A. Welch Foundation	United States	V-I-0002-20230731