9ZB9 | pdb_00009zb9

Cryo-EM Structure of Human GGPPS Bound to Selective Inhibitor CML-07-119

PDB DOI: https://doi.org/10.2210/pdb9ZB9/pdb
EM Map EMD-73979: EMDB EMDataResource

Classification: TRANSFERASE/INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-11-20 Released: 2026-09-09
Deposition Author(s): Ferens, F.G., Tsantrizos, Y.S., Lemieux, M.J.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada), Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 1.95 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9ZB9

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

Literature

Cryo-EM Structure of Human GGPPS Bound to Selective Inhibitor CML-07-119

Ferens, F.G., Tsantrizos, Y.S., Lemieux, M.J.

To be published.

Macromolecule Content

Total Structure Weight: 213.69 kDa
Atom Count: 13,724
Modeled Residue Count: 1,570
Deposited Residue Count: 1,806
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranylgeranyl pyrophosphate synthase	A B C D [auth F] E [auth G] A, B, C, D [auth F], E [auth G], F [auth H]	301	Homo sapiens	Mutation(s): 0 Gene Names: GGPS1 EC: 2.5.1 (PDB Primary Data), 2.5.1.1 (PDB Primary Data), 2.5.1.29 (PDB Primary Data), 2.5.1.10 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O95749 (Homo sapiens) Explore O95749 Go to UniProtKB: O95749
PHAROS: O95749 GTEx: ENSG00000152904
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O95749
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1C1E( Subject of Investigation/LOI) Query on A1C1E Download:Ideal Coordinates CCD File SDF format, chain W [auth G] SDF format, chain S [auth F] SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain G [auth A] SDF format, chain AA [auth H] MOL2 format, chain W [auth G] MOL2 format, chain S [auth F] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain AA [auth H] mmCIF format, chain W [auth G] mmCIF format, chain S [auth F] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain AA [auth H]	AA [auth H] G [auth A] K [auth B] O [auth C] S [auth F] AA [auth H], G [auth A], K [auth B], O [auth C], S [auth F], W [auth G]	{[(2-{3-[(3-fluoro-4-methoxyphenyl)carbamoyl]phenyl}thieno[2,3-d]pyrimidin-4-yl)amino]methylene}bis(phosphonic acid) C₂₁ H₁₉ F N₄ O₈ P₂ S XPPGEOUCUMGOGK-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth F] Focus chain W [auth G] Interactions & Density Focus chain AA [auth H] Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth F] Focus chain W [auth G]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain Z [auth G] SDF format, chain Y [auth G] SDF format, chain X [auth G] SDF format, chain V [auth F] SDF format, chain U [auth F] SDF format, chain T [auth F] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain DA [auth H] SDF format, chain CA [auth H] SDF format, chain BA [auth H] MOL2 format, chain Z [auth G] MOL2 format, chain Y [auth G] MOL2 format, chain X [auth G] MOL2 format, chain V [auth F] MOL2 format, chain U [auth F] MOL2 format, chain T [auth F] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain DA [auth H] MOL2 format, chain CA [auth H] MOL2 format, chain BA [auth H] mmCIF format, chain Z [auth G] mmCIF format, chain Y [auth G] mmCIF format, chain X [auth G] mmCIF format, chain V [auth F] mmCIF format, chain U [auth F] mmCIF format, chain T [auth F] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain DA [auth H] mmCIF format, chain CA [auth H] mmCIF format, chain BA [auth H]	BA [auth H] CA [auth H] DA [auth H] H [auth A] I [auth A] BA [auth H], CA [auth H], DA [auth H], H [auth A], I [auth A], J [auth A], L [auth B], M [auth B], N [auth B], P [auth C], Q [auth C], R [auth C], T [auth F], U [auth F], V [auth F], X [auth G], Y [auth G], Z [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth H] Focus chain CA [auth H] Focus chain DA [auth H] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth F] Focus chain U [auth F] Focus chain V [auth F] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth H] Focus chain CA [auth H] Focus chain DA [auth H] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth F] Focus chain U [auth F] Focus chain V [auth F] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth G]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 1.95 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	2.0_5729
RECONSTRUCTION	cryoSPARC

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-09

Deposition Author(s):

Tsantrizos, Y.S.

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-2023-04396
Canadian Institutes of Health Research (CIHR)	Canada	PJT-159743

Revision History (Full details and data files)

Version 1.0: 2026-09-09
Type: Initial release

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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.