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(A) Pairwise RMSD matrix table <t>of</t> <t>NDM-1</t> structures superimposed with force realignment method and refine with Gaussian Weights in <t>MOE.</t> PDB codes for structures with hydrolyzed substrate in the active site are highlighted in red. (B) Superposition of the 22 NDM-1 structures. 3S0Z, 4GYU, 4GYQ, 3SPU, and 3Q6X2 are highlighted in thick line and colored as shown in the index panel. (C) The RMSD-residue index 3D waterfall plots of NDM-1 structures compared with 3Q6X structure. (D) Superimposition of the active site among the reported NDM-1 structures (without 3S0Z and NDM-1 mutants 4GYQ and 4GYU) showing the metal chelating residues (Oliver) and conserved water molecules (Red) in the active site of NDM-1 structures. Residues from 3Q6X are highlighted in green.
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(A) Pairwise RMSD matrix table <t>of</t> <t>NDM-1</t> structures superimposed with force realignment method and refine with Gaussian Weights in <t>MOE.</t> PDB codes for structures with hydrolyzed substrate in the active site are highlighted in red. (B) Superposition of the 22 NDM-1 structures. 3S0Z, 4GYU, 4GYQ, 3SPU, and 3Q6X2 are highlighted in thick line and colored as shown in the index panel. (C) The RMSD-residue index 3D waterfall plots of NDM-1 structures compared with 3Q6X structure. (D) Superimposition of the active site among the reported NDM-1 structures (without 3S0Z and NDM-1 mutants 4GYQ and 4GYU) showing the metal chelating residues (Oliver) and conserved water molecules (Red) in the active site of NDM-1 structures. Residues from 3Q6X are highlighted in green.
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(A) Pairwise RMSD matrix table <t>of</t> <t>NDM-1</t> structures superimposed with force realignment method and refine with Gaussian Weights in <t>MOE.</t> PDB codes for structures with hydrolyzed substrate in the active site are highlighted in red. (B) Superposition of the 22 NDM-1 structures. 3S0Z, 4GYU, 4GYQ, 3SPU, and 3Q6X2 are highlighted in thick line and colored as shown in the index panel. (C) The RMSD-residue index 3D waterfall plots of NDM-1 structures compared with 3Q6X structure. (D) Superimposition of the active site among the reported NDM-1 structures (without 3S0Z and NDM-1 mutants 4GYQ and 4GYU) showing the metal chelating residues (Oliver) and conserved water molecules (Red) in the active site of NDM-1 structures. Residues from 3Q6X are highlighted in green.
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(A) Pairwise RMSD matrix table <t>of</t> <t>NDM-1</t> structures superimposed with force realignment method and refine with Gaussian Weights in <t>MOE.</t> PDB codes for structures with hydrolyzed substrate in the active site are highlighted in red. (B) Superposition of the 22 NDM-1 structures. 3S0Z, 4GYU, 4GYQ, 3SPU, and 3Q6X2 are highlighted in thick line and colored as shown in the index panel. (C) The RMSD-residue index 3D waterfall plots of NDM-1 structures compared with 3Q6X structure. (D) Superimposition of the active site among the reported NDM-1 structures (without 3S0Z and NDM-1 mutants 4GYQ and 4GYU) showing the metal chelating residues (Oliver) and conserved water molecules (Red) in the active site of NDM-1 structures. Residues from 3Q6X are highlighted in green.
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(A) Pairwise RMSD matrix table of NDM-1 structures superimposed with force realignment method and refine with Gaussian Weights in MOE. PDB codes for structures with hydrolyzed substrate in the active site are highlighted in red. (B) Superposition of the 22 NDM-1 structures. 3S0Z, 4GYU, 4GYQ, 3SPU, and 3Q6X2 are highlighted in thick line and colored as shown in the index panel. (C) The RMSD-residue index 3D waterfall plots of NDM-1 structures compared with 3Q6X structure. (D) Superimposition of the active site among the reported NDM-1 structures (without 3S0Z and NDM-1 mutants 4GYQ and 4GYU) showing the metal chelating residues (Oliver) and conserved water molecules (Red) in the active site of NDM-1 structures. Residues from 3Q6X are highlighted in green.

Journal: PLoS ONE

Article Title: Discovery of Novel New Delhi Metallo-β-Lactamases-1 Inhibitors by Multistep Virtual Screening

doi: 10.1371/journal.pone.0118290

Figure Lengend Snippet: (A) Pairwise RMSD matrix table of NDM-1 structures superimposed with force realignment method and refine with Gaussian Weights in MOE. PDB codes for structures with hydrolyzed substrate in the active site are highlighted in red. (B) Superposition of the 22 NDM-1 structures. 3S0Z, 4GYU, 4GYQ, 3SPU, and 3Q6X2 are highlighted in thick line and colored as shown in the index panel. (C) The RMSD-residue index 3D waterfall plots of NDM-1 structures compared with 3Q6X structure. (D) Superimposition of the active site among the reported NDM-1 structures (without 3S0Z and NDM-1 mutants 4GYQ and 4GYU) showing the metal chelating residues (Oliver) and conserved water molecules (Red) in the active site of NDM-1 structures. Residues from 3Q6X are highlighted in green.

Article Snippet: Hydrolyzed ampicillin, L-captopri, ampicillin and other 9 β-lactams (cefepime, cefotaxime, ceftazidime, cefuroxime, faropenem, imipenem, meropenem, penicillin G, piperacillin) structures downloaded from ZINC database were docked into the NDM-1 active site using different docking simulations in MOE and docking protocols in Discovery Studio (ADS, version 2.5; Accelrys Inc, San Diego, USA) according to the following procedure: the docking box was generated around the active site using the site finder module in MOE ( Figure B.B in ).

Techniques: Residue