2RAH

Human FDPS synthase in complex with novel inhibitor

PDB DOI: https://doi.org/10.2210/pdb2RAH/pdb

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

Deposited: 2007-09-15 Released: 2007-09-25
Deposition Author(s): Evdokimov, A.G., Barnett, B.L., Ebetino, F.H., Pokross, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.258
R-Value Work: 0.217
R-Value Observed: 0.219

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Human FDPS synthase in complex with novel inhibitor

Evdokimov, A.G., Barnett, B.L., Ebetino, F.H., Pokross, M.

To be published.

Macromolecule Content

Total Structure Weight: 43.9 kDa
Atom Count: 2,918
Modelled Residue Count: 340
Deposited Residue Count: 378
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesyl pyrophosphate synthetase	A	378	Homo sapiens	Mutation(s): 0 Gene Names: FDPS, FPS, KIAA1293 EC: 2.5.1.1 (PDB Primary Data), 2.5.1.10 (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 Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
11P Query on 11P Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	[(7R)-6,7-dihydro-5H-cyclopenta[c]pyridin-7-yl(hydroxy)methylene]bis(phosphonic acid) C₉ H₁₃ N O₇ P₂ WBALRBOBYFLYPZ-MRVPVSSYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
11P	BindingDB: 2RAH	IC50: 629.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.258
R-Value Work: 0.217
R-Value Observed: 0.219
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.171	α = 90
b = 111.171	β = 90
c = 70.44	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-09-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-09-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description

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Deposit Data

Help and Resources

2RAH

Human FDPS synthase in complex with novel inhibitor

Human FDPS synthase in complex with novel inhibitor

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)