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Variability in docking success rates due to dataset preparation.
(2012) J Comput Aided Mol Des 26
PubMed: 22566074 | PubMedCentral: PMC3397132 | DOI: 10.1007/s10822-012-9570-1
After the ACS-session the organizers discovered that 3 of the 85 structures (1GPK, 1HVY and 1S3V) had inverted ligand stereochemistry when compared to the PDB structures.
Table 6 Docking failures on corrected ACS-Astex set PDB code Failure type Minimum RMSD (Å) Present in binding site Top 1 Top 30 Water Metal 1g9v Placement 2.51 2.24 X 1gm8 Placement 3.20 2.69 X 1hp0 Scoring 2.93 1.07 X 1hvy Scoring 2.13 1.39 X 1jd0 Scoring 4.96 1.68 X 1l2s Scoring 3.65 0.80 1mzc Placement 3.66 2.92 X 1n2v Scoring 2.23 1.14 1oq5 Scoring 3.47 1.00 X 1owe Scoring 3.18 1.09 X 1q1 g Scoring 2.28 1.91 X 1r58 Placement 2.86 2.84 1sq5 Placement 4.96 2.55 X 1xm6 Scoring 2.40 0.50 X X 1y6b Placement 4.72 2.97 1ygc Placement 3.04 3.04 X Nearly half of the failure cases (8) were due to placement failure, where the docker was unable to generate any pose under 2 Å RMSD.
Table 2 Complexes requiring capping of chain termini or chain breaks Complexes requiring capping of chain termini 1GKC 1MEH 1Q41 1V48 1GM8 1 MMV 1R55 1V4S 1GPK 1 MZC 1R9O 1W1P 1HNN 1N1M 1S19 1W2G 1HP0 1N2J 1SJ0 1XM6 1HWI 1N2V 1SQN 1XOQ 1HWW 1N46 1T46 1XOZ 1IG3 1OF1 1T9B 1Y6B 1J3J 1OF6 1TT1 1YGC 1JD0 1OPK 1TZ8 1YQY 1JJE 1OQ5 1U1C 1YV3 1JLA 1OYT 1U4D 1YVF 1K3U 1P2Y 1UML 1YWR 1LPZ 1P62 1UNL 2BM2 1LRH 1PMN 1UOU 2BR1 1M2Z 1Q1G 1V0P 2BSM Complexes requiring capping of chain breaks 1GPK 1N46 1SJ0 1V48 1HP0 1NAV 1SQ5 1W2G 1HWI 1OF1 1SQN 1XM6 1J3J 1OF6 1T46 1XOQ 1JLA 1OYT 1T9B 1Y6B 1KE5 1P62 1U1C 1YV3 1L2S 1PMN 1U4D 1YWR 1MEH 1Q41 1UOU 1Z95 1MMV 1R9O 1V0P 2BR1 The ‘corrected’ ACS-Astex dataset After the session transpired at the ACS meeting, 3 structures from the ACS-Astex set (1GPK, 1HVY and 1S3V) were identified as containing an inverted stereocenter in the original dataset given to the participants compared to the original PDB structure.
After re-docking with the corrected ligand stereochemistry 1GPK and 1S3V successfully docked with better scores and RMSDs (RMSD of top 1: 1GPK = 0.31 Å, 1S3V = 0.39 Å), while 1HVY remained unimproved for the top 1 pose.
Table 1 Complexes requiring additional preparation Inconsistent stereo configuration 1GKC 1L7F 1R55 1VCJ 1GM8 1M2Z 1R58 1W1P 1GPK 1MMV 1R9O 1W2G 1HP0 1OF1 1S19 1X8X 1HVY 1OF6 1S3V 1XM6 1HWI 1OYT 1SQ5 1YGC 1HWW 1P2Y 1SQN 1YQY 1K3U 1P62 1TT1 1YV3 1KE5 1Q1G 1UML 1YWR 1KZK 1R1H 1V0P Co-factors with incorrect number of hydrogens 1G9V 1KZK 1Q1G 1W1P 1HWI 1M2Z 1Q4G 1W2G 1IA1 1MMV 1R9O 1XM6 1J3J 1OPK 1T9B 1XOQ 1JJE 1P62 1TZ8 Alternate locations missing hydrogens 1GM8 1OPK 1T9B 1XOZ 1HNN 1OQ5 1TZ8 1Y6B 1HP0 1Q4G 1UOU 1YV3 1IA1 1R1H 1VCJ 1YWR 1KZK 1S19 1W1P 1Z95 1L2S 1S3V 1X8X 2BR1 1N46 1T46 1XOQ The ‘modified’ ACS-Astex dataset Upon closer examination of some of the complexes it was noted that the hydrogen bond network was not optimal and therefore further optimization was warranted.
However, docking the corrected 1HVY ligand did produce a pose under 2 Å RMSD in the top 30 (RMSD of top 30 = 1.39 Å), and thus improved the top 30 result.
Publication Year: 2012
An innovative strategy for dual inhibitor design and its application in dual inhibition of human thymidylate synthase and dihydrofolate reductase enzymes.
(2013) PLoS One 8
PubMed: 23577115 | PubMedCentral: PMC3618229 | DOI: 10.1371/journal.pone.0060470
While, crystal structure with PDB ID of 1HVY co-crystallized with potent inhibitor TOMUDEX at a resolution of 1.9 Å was used for human TS enzyme  .
The starting proteins for hTS and hDHFR were prepared from their high resolution crystal structures (PDB ID: 1HVY for hTS, PDB ID: 1U72 for hDHFR) deposited in the Protein Data Bank.
Publication Year: 2013
Advances in the REDCAT software package.
(2013) BMC Bioinformatics 14
PubMed: 24098943 | PubMedCentral: PMC3840585 | DOI: 10.1186/1471-2105-14-302
To generate RDC data that reflect internal dynamics, a simulation utilizing chain A of the PDB:1HVY structure [ 81 ] was created by fixing the entire protein, with the exception of the eukaryotic inse... t and active site loop regions and 7 residues before and after each region (100 to 135 and 174 to 204, respectively).
The original structure of the hTS protein (PDB:1HVY) was loaded into REDCAT along with the averaged RDC data, which resulted from the simulation.
Treatment of acute lymphoblastic leukemia from traditional chinese medicine.
(2014) Evid Based Complement Alternat Med 2014
PubMed: 25136372 | PubMedCentral: PMC4055129 | DOI: 10.1155/2014/601064
Virtual Screening The receptors, human dihydrofolate reductase (DHFR) and human thymidylate synthase (TS) proteins were downloaded from Protein Data Bank of 1U72 (PDB ID: 1U72) [ 70 ] and 1HVY (PDB ID... 1HVY) [ 71 ].
Publication Year: 2014
Crystal structure of mouse thymidylate synthase in tertiary complex with dUMP and raltitrexed reveals N-terminus architecture and two different active site conformations.
(2014) Biomed Res Int 2014
PubMed: 24995339 | PubMedCentral: PMC4065713 | DOI: 10.1155/2014/945803
However, the “contributions” of the closed and open conformations are different in the two dimers, with the dimer AB resembling more closely the closed conformation seen in the 1HVY st... ucture (with the C α RMSD values for mTS-dUMP-Raltitrexed (chain A, residues 21–307) versus 1HVY (chain A, residues 27–313) and versus 2TSR (chain A, residues 21–301) being 0.368 Å and 0.750 Å, resp.)
and dimer CD resembling closer the open conformation seen in the 2TSR structure (with C α RMSD for mTS-dUMP-Raltitrexed (chain C, residues 21–307) versus 1HVY (chain A, residues 27–313) and versus 2TSR (chain A, residues 21–301) being 0.857 Å and 0.474 Å, resp.)
The comparison of both dimers with previously described analogous complexes of E. coli TS ( Ec TS, PDB ID: 2KCE) [ 17 ], populating the closed conformation, C. elegans TS ( Ce TS, PDB ID: 4IQQ; unpublished), populating the open conformation, rat TS (rTS, PDB ID: 2TSR) [ 4 ], populating the open conformation and two complexes of human TS, one populating the closed conformation (hTS, PDB ID: 1HVY) [ 6 ] and the other one the open conformation (hTS, PDB ID: 1I00) [ 5 ], indicates a mixed (partly closed and partly open) character of the active site conformations observed in both dimers of the mouse enzyme.
Analysis of mRNA recognition by human thymidylate synthase.
(2014) Biosci Rep 34
PubMed: 25423174 | PubMedCentral: PMC4274661 | DOI: 10.1042/BSR20140137
Apart from the previously observed conformational distinction around the loop I108-G129, the peptide K107-E128 was disordered in the high salt structure but adopted a well-defined helix–loop... 02013;helix motif in the low salt structure ( Figure 2 ) as previously observed in the R163K mutant [ 29 ] and the ternary complex (PDB: 1HVY) [ 30 ].
The hTS structure determined at low salt (PDB: 4H1I) represents the first time that the ligand-free protein has been captured in the active conformation, which was previously observed only in a mutant containing the stabilizing mutation R163K (PDB: 2RD8) [ 29 ] and in substrate complexes, including a ternary complex of the enzyme with dUMP as well as the folic acid analogue inhibitor raltitrexed (PDB: 1HVY) [ 30 ].
( B ) Side view: superposition of hTS in the active conformation (blue, PDB code 1HVY) which had been crystallized in complex with the folic acid analogue inhibitor raltitrexed (green) and dUMP substrate (cyan) covalently bound at the active site residue C195.
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