CADD Project Report 學號: 姓名:.

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1 CADD Project Report 學號: 姓名:

2 # Name Protein PDBID Ligand 1 柯宏欣 黃翎瑄 1-10 2 姚秉宏 劉守軒 11-20 3 張景富 曾賀德 21-30 4 徐　綾 蕭廷怡 31-40 5 崔雁茹 戴若雲 41-50 # Name Protein PDBID Ligand 6 鍾妮津 許芯緁 51-60 7 張哲綱 柯廷揚 61-70 8 許潔馨 鄭宇倫 71-80 9 王靖涵 柯紹文 81-90 10 姚佳伶 周昱吟 91-100

3 Target Protein Compounds 990

4 Protein: cav1aaq_PSI.pdb Ligand : pdb1aaq_PSI.mol +
1 2 2 Test Set : 990 Ligands ZINC Database Protein: cav1aaq_PSI.pdb Ligand : pdb1aaq_PSI.mol + 4 5 9 iGemDock (Standard) Rank: 3/991 Similar Compound Search (Tanimoto-60) 8 10 991 Docked Pose Top 15 Compounds 10 compounds 6 11 SiMMap iGemDock (Accurate) 7 Anchors Top 5 Compounds 13 12 PDB Docking Pocket Analysis(PyMol) Post-screening Analysis 3 14 Mechanism of Drug Actions Conclusion

5 Target Protein and Ligand
4dfr MTX

6 Introduction of Target Protein
1 What is this protein? (from paper) How many chains? Please show the secondary structure. Are there any disulfide bonds? 4dfr

7 NMDA receptors are the Glutamate receptor ionotropic

8 指令： color by chain 兩種顏色代表含有兩條chain A chain：green B chain：blue

9 針對A、B chain 紅色代表 a-helix (共含有17條) 黃色代表 b-sheet(共含有29條) 綠色代表 loop (共含有42條)

10 Disulfide bonds

11 Ligand present 2 GLU C5 H9 N O4

12 Mechanism of Drug Actions
3 Nature vol 438|10 Nov. 2005|doi: /nature04089

13 Nature vol 438|10 Nov. 2005|doi:10.1038/nature04089

14 Molecular Docking Using iGEMDOCK
4 Standard Docking

15 Rank 5

16 SiMMap 6

17 SiMMap Anchors 7 G186 G185 V1 E1 PLP R135 F55 MLI E2 K56

18 Top15 Compounds from 990 set 8 # Ligand ID Energy 1 MFCD00000058 11 2
12 3 13 4 14 5 15 6 7 8 9 10

19 Similar Compound Search
9 Tanimoto-60

20 10 Compounds from similarity search
2 # Ligand ID 1 ZINC895124 2 ZINC901627 3 ZINC901628 4 ZINC901823 5 ZINC 6 ZINC 7 ZINC 8 ZINC 9 ZINC 10 ZINC 3 4

21 5 6 7 8 9 10

22 Molecular Docking Using iGEMDOCK
11 Accurate Docking

23 Post-screening Analysis
12 Table of Docking Energy Figure of Docking Energy Interaction Profile Interaction Analysis

24 Table of Docking Energy
1 11 -89.2 2 12 3 13 -99.29 4 -99.02 14 5 -109 15 -91.11 6 -96.6 -92.35 7 -97.21 -98.28 8 -88.91 9 -109.3 10 -107.9

25 Figure of Docking Energy
Energy Compound

26 Interaction Profile of Top5

27 Interaction Analysis of Top5
18 34 19 49 28 2 紅色部分是指靠電子吸引的鍵結 綠色部分是指靠氫鍵的鍵結 灰色部分是指靠凡得瓦力的鍵結

28 Top1 13  4-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)-4-pyridyl]methyleneamino]butanoic K56 R135 G186 G185 F55 E1 E2 V1 ZINC

29 Top2  4-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)-4-pyridyl]methyleneamino]butanoic K56 R135 G186 G185 F55 E1 E2 V1 ZINC

30 Top3  4-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)-4-pyridyl]methyleneamino]butanoic K56 R135 G186 G185 F55 E1 E2 V1 ZINC

31 Top4  4-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)-4-pyridyl]methyleneamino]butanoic K56 R135 G186 G185 F55 E1 E2 V1 ZINC

32 Top5  4-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)-4-pyridyl]methyleneamino]butanoic K56 R135 G186 G185 F55 E1 E2 V1 ZINC

33 Conclusion 14