Primary Citation PubMed: 15289103
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Analysis of X-ray structures of matrix metalloproteinases via chaotic map clustering.
(2010) BMC Bioinformatics 11
PubMed: 20932281 | PubMedCentral: PMC3098083 | DOI: 10.1186/1471-2105-11-500
sub-families classes PDB codes archetypal MMPs MMP-1 1CGE, 966C, 1HFC, 2TCL, 1CGL, 1CGF, 2J0T Collagenasi MMP-8 1MNC, 1ZS0, 1ZP5, 1MMB, 1JAO, 1JAP, 1JAQ, 1JJ9, 1I76, 1I73, 1ZVX, 1BZS, 1KBC, 1JAN, 1A86... 1A85, 1JH1, 3DNG, 3DPE, 3DPF, 2OY2, 2OY4 MMP-13 1XUC, 1XUR, 1XUD, 1YOU, 830C, 456C, 1ZTQ, 2D1N, 1CXV, 2PJT, 2OW9, 2E2D, 2OZR metallo-elastase MMP-12 1Y93, 1RMZ, 1OS9, 1OS2, 1UTZ, 1UTT, 1JIZ, 1ROS, 1JK3, 3F15, 3F16, 3F17, 3F18, 3F19, 3F1A, 2W0D, 2HU6, 2OXU, 2OXW, 2OXZ Stromelysin MMP-3 1B8Y, 1CIZ, 1CAQ, 1G4K, 2USN, 1USN, 1SLM, 1UEA, 1HFS, 1QIC, 1C3I, 1CQR, 1BQO, 1BIW, 1SLN, 1HY7, 1G05, 1G49, 1D5J, 1D8F, 1D7X, 1D8M, 2D1O, 1B3D, 1QIA, 1C8T MMP-10 1Q3A matrilysin Matrilysin MMP-7 1MMP, 1MMQ, 1MMR gelatinases Gelatinase MMP-9 1GKC, 1GKD, 2OVX, 2OVZ, 2OW0, 2OW1, 2OW2 MMP-2 1QIB convertase-activatable MMPs MT-MMPs MMP-14 1BUV, 1BQQ MMP-16 1RM8 stromelysin-3 MMP-11 1HV5 After removing water molecules and co-crystallised inhibitors, MMPs were aligned onto Cartesian coordinates of C-alpha atoms and the three catalytic histidine side chains of 1ZS0, selected as template.
Inhibitors with bulkier moieties (e.g., 4-(4-phenyl-piperidin-1-yl)-benzenesulfonylamino and 4'-[(benzofuran-2-carbonyl)-amino]-biphenyl-4-sulfonylamino substituents) were effectively comprised in the same cluster intercepting deep pocket MMP complexes (i.e., PDB: 1B8Y , PDB: 1CIZ and PDB: 1CAQ as MMP-3, PDB: 1ZTQ and PDB: 1ROS as MMP-12).
Publication Year: 2010
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