Download MendeleyCrystal structure of human farnesyl pyrophosphate synthase in complex with a cryptic pocket ligand, JDS05120
Pandya, V.R., Park, J.To be published.
9CY2 | pdb_00009cy2
Crystal structure of human farnesyl pyrophosphate synthase in complex with a cryptic pocket ligand, JDS05120
- PDB DOI: https://doi.org/10.2210/pdb9CY2/pdb
- Classification: TRANSFERASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2024-08-01 Released: 2025-10-29
- Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.246 (Depositor), 0.265 (DCC)
- R-Value Work: 0.188 (Depositor), 0.212 (DCC)
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Farnesyl pyrophosphate synthase | A [auth F] | 375 | Homo sapiens | Mutation(s): 0 Gene Names: FDPS, FPS, KIAA1293 EC: 2.5.1.10 (PDB Primary Data), 2.5.1.1 (PDB Primary Data) |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P14324 (Homo sapiens) Explore P14324 Go to UniProtKB: P14324 | |||||
PHAROS: P14324 GTEx: ENSG00000160752 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P14324 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| JD5 (Subject of Investigation/LOI) Query on JD5 | C [auth F] | [({5-[4-(cyclopropyloxy)phenyl]pyridin-3-yl}amino)methanediyl]bis(phosphonic acid) C15 H18 N2 O7 P2 QCLQOQRSHDMFKS-UHFFFAOYSA-N |  | ||
| PO4 Query on PO4 | B [auth F] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.246 (Depositor), 0.265 (DCC)
- R-Value Work: 0.188 (Depositor), 0.212 (DCC)
Space Group: P 41 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 110.95 | α = 90 |
| b = 110.95 | β = 90 |
| c = 73.9 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| REFMAC | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-10-29 Deposition Author(s): Pandya, V.R., Park, J.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Natural Sciences and Engineering Research Council (NSERC, Canada) | Canada | RGPIN-2020-04281 |
Revision History (Full details and data files)
- Version 1.0: 2025-10-29
Type: Initial release
