9IG9 | pdb_00009ig9

FSP1 (tetrapod ancestor) bound to FAD and NAD+ and compound 3

PDB DOI: https://doi.org/10.2210/pdb9IG9/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mammalia
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2025-02-19 Released: 2026-03-04
Deposition Author(s): Cecchini, D., Mattevi, A.
Funding Organization(s): European Research Council (ERC), Italian Association for Cancer Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.265 (Depositor), 0.270 (DCC)
R-Value Work:
0.215 (Depositor), 0.227 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

AI-enhanced adaptive virtual screening of large libraries for ligand discovery.

Cecchini, D., Nigam, A., Tang, M., Reis, J., Koop, M., Gottinger, A., Nicoll, C.R., Wang, Y., Jayaraj, A., Cinaroglu, S.S., Torner, R., Malets, Y., Gehev, M., Padmanabha Das, K.M., Churion, K., Kim, J., Thomas, N., Li, Y., Seo, H.S., Dhe-Paganon, S., Secker, C., Haddadnia, M., Hasson, A., Li, M., Kumar, A., Levin-Konigsberg, R., Choi, E.B., Shapiro, G.I., Cox 3rd, H., Sebastian, L., Braithwaite, C., Bashyal, P., Radchenko, D.S., Kumar, A., Yang, L., Aquilanti, P.Y., Gabb, H., Alhossary, A., O'Neill, E., Wagner, G., Aspuru-Guzik, A., Moroz, Y.S., Kalodimos, C.G., Fackeldey, K., Schuetz, J.D., Mattevi, A., Arthanari, H., Gorgulla, C.

(2026) Nat Biotechnol

PubMed: 42680826 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41587-026-03217-x
Primary Citation Related Structures:
9IFT, 9IFU, 9IFW, 9IFY, 9IFZ, 9IG9, 9QRT, 9S0V

PubMed Abstract:
Ultralarge virtual screenings (ULVSs) evaluate billions of molecules for drug discovery but face cost, flexibility and scalability limits. We introduce AdaptiveFlow, an open-source platform that makes ULVSs more accessible, scalable and efficient and supports artificial intelligence (AI) and machine learning (ML) method development. AdaptiveFlow provides a screening-ready version of the Enamine REAL Space, to our knowledge the largest library of ready-to-dock, drug-like molecules, comprising 69 billion compounds, also available in SELFIES format. An 18-dimensional grid of molecular properties prioritizes promising chemical subspaces, with optional active learning, reducing computational costs by orders of magnitude. AdaptiveFlow integrates >1,500 docking protocols, including GPU-accelerated and ML-based methods, and achieves near-linear scaling on up to 5.6 million CPUs in the Amazon Web Services cloud. We identified nanomolar inhibitors of two disease-relevant targets, ferroptosis suppressor protein 1 (FSP1) and poly(ADP-ribose) polymerase 1. Co-crystal structures provided mechanistic insights into FSP1 inhibition. AdaptiveFlow enables drug discovery at unprecedented scale and supports the development of AI-driven methods.

Organizational Affiliation

Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.

Department of Computer Science, Stanford University, Stanford, CA, USA.

Frazer Institute, Faculty of Medicine at the Translational Research Institute Australia, The University of Queensland, Brisbane, Queensland, Australia.

School of Biomedical Sciences, Centre for Genomics and Personalised Health at the Translational Research Institute Australia, Queensland University of Technology, Brisbane, Queensland, Australia.

Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.

Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.

Amazon Web Services, Seattle, WA, USA.

Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA.

Department of Biochemistry, University of Oxford, Oxford, UK.

Department of Bioengineering, Ege University, Bornova, Türkiye.

Department of Chemistry, University of Zurich, Zurich, Switzerland.

V. P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Science of Ukraine, Kyiv, Ukraine.

Google, Mountain View, CA, USA.

Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA.

Chemical Biology Program, Dana-Farber Cancer Institute, Boston, MA, USA.

Zuse Institute Berlin (ZIB), Berlin, Germany.

Max Delbrück Center for Molecular Medicine, Berlin, Germany.

Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.

Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada.

Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.

Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.

Mathematical Institute, University of Oxford, Oxford, UK.

Department of Oncology, University of Oxford, Oxford, UK.

Harvard College, Cambridge, MA, USA.

Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India.

Department of Genetics, Stanford University, Stanford, CA, USA.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.

Enamine Ltd, Kyiv, Ukraine.

Institute for Mathematics, Technical University Berlin, Berlin, Germany.

NVIDIA, Santa Clara, CA, USA.

Intel, Santa Clara, CA, USA.

Wesleyan University, Middletown, CT, USA.

Pulse for Integrated Solutions, Unterschleißheim, Germany.

Canadian Institute for Advanced Research, Toronto, Ontario, Canada.

Department of Materials Science & Engineering, University of Toronto, Toronto, Ontario, Canada.

Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.

NVIDIA, Toronto, Ontario, Canada.

Acceleration Consortium, Acceleration Consortium, Toronto, Ontario, Canada.

Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.

Taras Shevchenko National University of Kyiv, Kyiv, Ukraine.

Chemspace, Kyiv, Ukraine.

Department of Biology and Biotechnology, University of Pavia, Pavia, Italy. andrea.mattevi@unipv.it.

Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA. hari@hms.harvard.edu.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA. hari@hms.harvard.edu.

Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA. hari@hms.harvard.edu.

Broad Institute of MIT and Harvard, Cambridge, MA, USA. hari@hms.harvard.edu.

Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA. christoph.gorgulla@stjude.org.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA. christoph.gorgulla@stjude.org.

Macromolecule Content

Total Structure Weight: 83.63 kDa
Atom Count: 6,003
Modeled Residue Count: 729
Deposited Residue Count: 736
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FSP1 (tetrapod ancestor)	A, B	368	Mammalia	Mutation(s): 0 EC: 1.6.5
UniProt
Find proteins for E1BR24 (Gallus gallus) Explore E1BR24 Go to UniProtKB: E1BR24
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E1BR24
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain C [auth A]	C [auth A], J [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain D [auth A]	D [auth A], K [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [auth B]
A1I34 (Subject of Investigation/LOI) Query on A1I34 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain E [auth A]	E [auth A], L [auth B]	~{N}-[3-[4-(5-phenyl-4~{H}-1,2,4-triazol-3-yl)piperidin-1-yl]carbonylphenyl]benzamide C₂₇ H₂₅ N₅ O₂ PMGKFAXGJYRVER-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]