3KEE

HCV NS3/NS4A complexed with Non-covalent macrocyclic compound TMC435

• PDB DOI: https://doi.org/10.2210/pdb3KEE/pdb

• Classification: HYDROLASE
• Organism(s): Hepacivirus hominis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-26 Released: 2010-03-09 
• Deposition Author(s): Lindberg, J.D., Nystrom, S., Cummings, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.246 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 

Literature

Induced-Fit Binding of the Macrocyclic Noncovalent Inhibitor TMC435 to its HCV NS3/NS4A Protease Target

Cummings, M.D., Lindberg, J.D., Lin, T.-I., de Kock, H., Lenz, O., Lilja, E., Fellander, S., Baraznenok, V., Nystrom, S., Nilsson, M., Vrang, L., Edlund, M., Rosenquist, A., Samuelsson, B., Raboisson, P., Simmen, K.

(2010) Angew Chem Int Ed Engl 49: 1652-1655

• PubMed: 20166108 
• DOI: https://doi.org/10.1002/anie.200906696
• Primary Citation of Related Structures:  
  3KEE, 3KF2

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Organizational Affiliation: 

Tibotec BVBA, Gen De Wittelaan L 11B 3, 2800 Mechelen, Belgium. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 93.63 kDa 
• Atom Count: 5,877 
• Modelled Residue Count: 760 
• Deposited Residue Count: 852 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A, C [auth B], E [auth C], G [auth D]	190	Hepacivirus hominis	Mutation(s): 0  EC: 3.4.21.98
UniProt
Find proteins for P90191 (Hepacivirus hominis) Explore P90191  Go to UniProtKB:  P90191

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
19-mer peptide from Genome polyprotein	B [auth E], D [auth F], F [auth G], H	23	Hepacivirus hominis	Mutation(s): 0
UniProt
Find proteins for Q6GYR8 (Hepacivirus hominis) Explore Q6GYR8  Go to UniProtKB:  Q6GYR8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
30B	I [auth A], K [auth B], M [auth C], P [auth D]	(2R,3aR,10Z,11aS,12aR,14aR)-N-(cyclopropylsulfonyl)-2-({7-methoxy-8-methyl-2-[4-(1-methylethyl)-1,3-thiazol-2-yl]quinolin-4-yl}oxy)-5-methyl-4,14-dioxo-2,3,3a,4,5,6,7,8,9,11a,12,13,14,14a-tetradecahydrocyclopenta[c]cyclopropa[g][1,6]diazacyclotetradecine-12a(1H)-carboxamide C38 H47 N5 O7 S2 JTZZSQYMACOLNN-VDWJNHBNSA-N
GOL	O [auth C], R [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	J [auth A], L [auth B], N [auth C], Q [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
30B	BindingDB:  3KEE	Ki: min: 0.36, max: 0.5 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.246 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.034	α = 92.44
b = 54.454	β = 93.16
c = 85.495	γ = 116.04

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-09 
Deposition Author(s): Lindberg, J.D., Nystrom, S., Cummings, M.D.

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description