3WV3: Catalytic domain of MMP-13

Crystal structure of the catalytic domain of MMP-13 complexed with N-(3-methoxybenzyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-2-carboxamide. Determined by X-ray diffraction at 1.6 Å resolution. Released 24 Sept 2014.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,198
Mol. weight: 39.79 kDa
Ligands: ZN, CA, WLL
Released: 24 Sept 2014

Explore 3WV3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3WV3 contains 9 α-helices and 18 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	106	1	1
α-helix	107-108	2
β-strand	117-122	6	2
α-helix	131-146	16
β-strand	152-156	5	2
β-strand	163-168	6	2
β-strand	186-188	3	2
α-helix	189-190	2
β-strand	199-202	4	2
β-strand	207-208	2	3
β-strand	214-215	2	3
α-helix	216-228	13
β-strand	230	1	4
α-helix	256-266	11

Chain B: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	106	1	4
β-strand	117-122	6	5
α-helix	131-146	16
β-strand	152-155	4	5
β-strand	163-168	6	5
β-strand	186-188	3	5
α-helix	189-190	2
β-strand	199-202	4	5
β-strand	207-208	2	6
β-strand	214-215	2	6
α-helix	216-228	13
β-strand	230	1	1
α-helix	256-266	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Collagenase 3	A, B	protein	171	Homo sapiens	P45452 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3WV3_1 Collagenase 3 (chains A, B)
YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADI
MISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHE
FGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPGDEDPN

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
CA	Calcium ion	Ca	4
WLL	N-(3-methoxybenzyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-2-carboxamide	C15 H13 N3 O3 S	2

Water and common crystallization additives (NA, FMT, EDO) are not listed.

Primary citation

Thieno[2,3-d]pyrimidine-2-carboxamides bearing a carboxybenzene group at 5-position: highly potent, selective, and orally available MMP-13 inhibitors interacting with the S1′′ binding site. Nara, H., Sato, K., Naito, T. et al. Bioorg Med Chem (2014) 22:5487-5505. DOI 10.1016/j.bmc.2014.07.025 · PubMed

Other PDB entries of the same protein (UniProt P45452 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5B5O 1.2 Å, Crystal structure of the catalytic domain of MMP-13 complexed with…
3ZXH 1.3 Å, MMP-13 complexed with 2-Napthylsulfonamide hydroxamic acid inhibitor
4JP4 1.43 Å, Mmp13 in complex with a reverse hydroxamate Zn-binder
5B5P 1.6 Å, Crystal structure of the catalytic domain of MMP-13 complexed with…
5UWK 1.6 Å, Matrix metalloproteinase-13 complexed with selective inhibitor compound (S)-10a
830C 1.6 Å, Collagenase-3 (mmp-13) complexed to a sulphone-based hydroxamic acid
5UWM 1.62 Å, Matrix metalloproteinase-13 complexed with selective inhibitor compound (R)-17a
4L19 1.66 Å, Matrix metalloproteinase-13 complexed with selective inhibitor compound Q1
1XUC 1.7 Å, Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor
2YIG 1.7 Å, MMP13 in complex with a novel selective non zinc binding inhibitor
6HV2 1.71 Å, MMP-13 in complex with the peptide IMISF
2OW9 1.74 Å, Crystal structure analysis of the MMP13 catalytic domain in complex with specific…

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