7U64 | pdb_00007u64

Crystal Structure of Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.225 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7U64

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structures of drug-specific monoclonal antibodies bound to opioids and nicotine reveal a common mode of binding.

Rodarte, J.V.Baehr, C.Hicks, D.Liban, T.L.Weidle, C.Rupert, P.B.Jahan, R.Wall, A.McGuire, A.T.Strong, R.K.Runyon, S.Pravetoni, M.Pancera, M.

(2023) Structure 31: 20-32.e5

  • DOI: https://doi.org/10.1016/j.str.2022.11.008
  • Primary Citation Related Structures: 
    7U61, 7U62, 7U63, 7U64

  • PubMed Abstract: 

    Opioid-related fatal overdoses have reached epidemic proportions. Because existing treatments for opioid use disorders offer limited long-term protection, accelerating the development of newer approaches is critical. Monoclonal antibodies (mAbs) are an emerging treatment strategy that targets and sequesters selected opioids in the bloodstream, reducing drug distribution across the blood-brain barrier, thus preventing or reversing opioid toxicity. We previously identified a series of murine mAbs with high affinity and selectivity for oxycodone, morphine, fentanyl, and nicotine. To determine their binding mechanism, we used X-ray crystallography to solve the structures of mAbs bound to their respective targets, to 2.2 Å resolution or higher. Structural analysis showed a critical convergent hydrogen bonding mode that is dependent on a glutamic acid residue in the mAbs' heavy chain and a tertiary amine of the ligand. Characterizing drug-mAb complexes represents a significant step toward rational antibody engineering and future manufacturing activities to support clinical evaluation.


  • Organizational Affiliation
    • Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.

Macromolecule Content 

  • Total Structure Weight: 441.95 kDa 
  • Atom Count: 33,436 
  • Modeled Residue Count: 3,942 
  • Deposited Residue Count: 4,005 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HY6-F9.6 Fab heavy chain
A, C, E, G, I
A, C, E, G, I, K, M, O, Q
226Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
HY6-F9.6 Fab light chain
B, D, F, H, J
B, D, F, H, J, L, N, P, R
219Mus musculusMutation(s): 0 

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7V7
(Subject of Investigation/LOI)

Query on 7V7



Download:Ideal Coordinates CCD File
DB [auth I]
EA [auth C]
HA [auth E]
IC [auth Q]
LB [auth K]
DB [auth I],
EA [auth C],
HA [auth E],
IC [auth Q],
LB [auth K],
QA [auth G],
S [auth A],
UB [auth M],
XB [auth O]
N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide
C22 H28 N2 O
PJMPHNIQZUBGLI-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
AA [auth B]
AB [auth H]
AC [auth O]
BA [auth B]
BB [auth H]
AA [auth B],
AB [auth H],
AC [auth O],
BA [auth B],
BB [auth H],
CA [auth B],
CB [auth H],
DA [auth B],
DC [auth P],
EB [auth I],
EC [auth P],
FA [auth C],
FB [auth I],
FC [auth P],
GC [auth P],
HC [auth P],
IB [auth J],
JA [auth E],
JB [auth J],
KA [auth E],
KB [auth J],
KC [auth Q],
LC [auth Q],
MA [auth F],
MC [auth Q],
NA [auth F],
NB [auth K],
NC [auth Q],
OA [auth F],
OB [auth K],
OC [auth Q],
PA [auth F],
QB [auth L],
QC [auth R],
RA [auth G],
RB [auth L],
RC [auth R],
SA [auth G],
SB [auth L],
SC [auth R],
T [auth A],
TB [auth L],
TC [auth R],
U [auth A],
UC [auth R],
V [auth A],
VB [auth M],
VC [auth R],
W [auth A],
WA [auth H],
WB [auth M],
X [auth A],
XA [auth H],
Y [auth B],
YA [auth H],
YB [auth O],
Z [auth B],
ZA [auth H],
ZB [auth O]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
BC [auth P]
CC [auth P]
GA [auth D]
GB [auth J]
HB [auth J]
BC [auth P],
CC [auth P],
GA [auth D],
GB [auth J],
HB [auth J],
IA [auth E],
JC [auth Q],
LA [auth F],
MB [auth K],
PB [auth L],
PC [auth R],
TA [auth H],
UA [auth H],
VA [auth H]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.225 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 218.139α = 90
b = 218.139β = 90
c = 89.023γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesUG3 DA047711

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-11
    Type: Initial release
  • Version 1.1: 2023-01-18
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary