4U01 | pdb_00004u01

HCV NS3/4A serine protease in complex with 6570

PDB DOI: https://doi.org/10.2210/pdb4U01/pdb

Classification: HYDROLASE
Organism(s): Hepatitis C virus (isolate Con1), Orthohepacivirus hominis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-07-11 Released: 2015-07-29
Deposition Author(s): Parsy, C.C., Alexandre, F.-R., Brandt, G., Caillet, C., Chaves, D., Derock, M., Gloux, D., Griffon, Y., Lallos, L.B., Leroy, F., Liuzzi, M., Loi, A.-G., Mayes, B., Moulat, L., Moussa, A., Chiara, M., Roques, V., Rosinovsky, E., Seifer, M., Stewart, A., Wang, J., Standring, D., Surleraux, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.290 (Depositor), 0.287 (DCC)
R-Value Work:
0.233 (Depositor), 0.234 (DCC)
R-Value Observed:
0.236 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Discovery and structural diversity of the hepatitis C virus NS3/4A serine protease inhibitor series leading to clinical candidate IDX320.

Parsy, C.C., Alexandre, F.R., Bidau, V., Bonnaterre, F., Brandt, G., Caillet, C., Cappelle, S., Chaves, D., Convard, T., Derock, M., Gloux, D., Griffon, Y., Lallos, L.B., Leroy, F., Liuzzi, M., Loi, A.G., Moulat, L., Chiara, M., Rahali, H., Roques, V., Rosinovsky, E., Savin, S., Seifer, M., Standring, D., Surleraux, D.

(2015) Bioorg Med Chem Lett 25: 5427-5436

PubMed: 26410074 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2015.09.009
Primary Citation Related Structures:
4U01

PubMed Abstract:
Exploration of the P2 region by mimicking the proline motif found in BILN2061 resulted in the discovery of two series of potent HCV NS3/4A protease inhibitors. X-ray crystal structure of the ligand in contact with the NS3/4A protein and modulation of the quinoline heterocyclic region by structure based design and modeling allowed for the optimization of enzyme potency and cellular activity. This research led to the selection of clinical candidate IDX320 having good genotype coverage and pharmacokinetic properties in various species.

Organizational Affiliation

IDENIX, a wholly-owned subsidiary of Merck & Co, 1682 rue de la Valsière, Cap Gamma, BP 50001, 34189 Montpellier Cedex 4, France. Electronic address: christophe.parsy@merck.com.

Macromolecule Content

Total Structure Weight: 215.98 kDa
Atom Count: 13,360
Modeled Residue Count: 1,755
Deposited Residue Count: 1,971
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural 3 protease	A B C D E A, B, C, D, E, F, G, H, I [auth J]	203	Hepatitis C virus (isolate Con1)	Mutation(s): 0
UniProt
Find proteins for Q9WMX2 (Hepatitis C virus genotype 1b (isolate Con1)) Explore Q9WMX2 Go to UniProtKB: Q9WMX2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WMX2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NS4A protein	J [auth K] K [auth L] L [auth M] M [auth N] N [auth O] J [auth K], K [auth L], L [auth M], M [auth N], N [auth O], O [auth P], P [auth Q], Q [auth T], R [auth U]	16	Orthohepacivirus hominis	Mutation(s): 0 Gene Names: NS4A
UniProt
Find proteins for F0UY39 (Hepacivirus hominis) Explore F0UY39 Go to UniProtKB: F0UY39
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F0UY39
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
39W Query on 39W Download:Ideal Coordinates CCD File SDF format, chain FA [auth F] SDF format, chain HA [auth G] SDF format, chain KA [auth H] SDF format, chain MA [auth J] SDF format, chain U [auth B] SDF format, chain X [auth C] SDF format, chain Z [auth D] SDF format, chain S [auth A] SDF format, chain CA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain KA [auth H] MOL2 format, chain MA [auth J] MOL2 format, chain U [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain S [auth A] MOL2 format, chain CA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain KA [auth H] mmCIF format, chain MA [auth J] mmCIF format, chain U [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain S [auth A] mmCIF format, chain CA [auth E]	CA [auth E] FA [auth F] HA [auth G] KA [auth H] MA [auth J] CA [auth E], FA [auth F], HA [auth G], KA [auth H], MA [auth J], S [auth A], U [auth B], X [auth C], Z [auth D]	(2S,3aS,10Z,11aS,12aR)-2-({8-fluoro-7-methoxy-2-[4-(propan-2-yl)-1,3-thiazol-2-yl]quinolin-4-yl}oxy)-5-methyl-N-[(1-methylcyclopropyl)sulfonyl]-4,14-dioxo-1,2,3,3a,4,5,6,7,8,9,11a,12,13,14-tetradecahydro-12aH-cyclopropa[m]pyrrolo[1,2-c][1,3,6]triazacyclotetradecine-12a-carboxamide C₃₇ H₄₅ F N₆ O₇ S₂ WCUAGYIETHEUQO-MULYSJGUSA-N		Interactions Focus chain CA [auth E] Focus chain FA [auth F] Focus chain HA [auth G] Focus chain KA [auth H] Focus chain MA [auth J] Focus chain S [auth A] Focus chain U [auth B] Focus chain X [auth C] Focus chain Z [auth D] Interactions & Density Focus chain CA [auth E] Focus chain FA [auth F] Focus chain HA [auth G] Focus chain KA [auth H] Focus chain MA [auth J] Focus chain S [auth A] Focus chain U [auth B] Focus chain X [auth C] Focus chain Z [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain LA [auth H] SDF format, chain NA [auth J] SDF format, chain T [auth A] SDF format, chain V [auth B] SDF format, chain Y [auth C] SDF format, chain IA [auth G] SDF format, chain GA [auth F] SDF format, chain DA [auth E] SDF format, chain AA [auth D] MOL2 format, chain LA [auth H] MOL2 format, chain NA [auth J] MOL2 format, chain T [auth A] MOL2 format, chain V [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain IA [auth G] MOL2 format, chain GA [auth F] MOL2 format, chain DA [auth E] MOL2 format, chain AA [auth D] mmCIF format, chain LA [auth H] mmCIF format, chain NA [auth J] mmCIF format, chain T [auth A] mmCIF format, chain V [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain IA [auth G] mmCIF format, chain GA [auth F] mmCIF format, chain DA [auth E] mmCIF format, chain AA [auth D]	AA [auth D] DA [auth E] GA [auth F] IA [auth G] LA [auth H] AA [auth D], DA [auth E], GA [auth F], IA [auth G], LA [auth H], NA [auth J], T [auth A], V [auth B], Y [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain DA [auth E] Focus chain GA [auth F] Focus chain IA [auth G] Focus chain LA [auth H] Focus chain NA [auth J] Focus chain T [auth A] Focus chain V [auth B] Focus chain Y [auth C] Interactions & Density Focus chain AA [auth D] Focus chain DA [auth E] Focus chain GA [auth F] Focus chain IA [auth G] Focus chain LA [auth H] Focus chain NA [auth J] Focus chain T [auth A] Focus chain V [auth B] Focus chain Y [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain W [auth B] SDF format, chain JA [auth G] SDF format, chain BA [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain W [auth B] MOL2 format, chain JA [auth G] MOL2 format, chain BA [auth D] mmCIF format, chain EA [auth E] mmCIF format, chain W [auth B] mmCIF format, chain JA [auth G] mmCIF format, chain BA [auth D]	BA [auth D], EA [auth E], JA [auth G], W [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth D] Focus chain EA [auth E] Focus chain JA [auth G] Focus chain W [auth B] Interactions & Density Focus chain BA [auth D] Focus chain EA [auth E] Focus chain JA [auth G] Focus chain W [auth B]