Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T81623 | Target Info | |||
| Target Name | Death-associated protein kinase 3 (DAPK3) | ||||
| Synonyms | Zipper-interacting protein kinase; ZIPK; ZIP-kinase; MYPT1 kinase; DAP-like kinase; DAP kinase 3 | ||||
| Target Type | Literature-reported Target | ||||
| Gene Name | DAPK3 | ||||
| Biochemical Class | Kinase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: CMP-6 | Ligand Info | |||||
| Structure Description | Crystal structure of human ZIP kinase in complex with a tetracyclic pyridone inhibitor (Pyridone 6) | PDB:2J90 | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [1] |
| PDB Sequence |
FQSMVEDHYE
14 MGEELGSGQF24 AIVRKCRQKG34 TGKEYAAKFI44 KKRRLSSRRG55 VSREEIEREV 65 NILREIRHPN75 IITLHDIFEN85 KTDVVLILEL95 VSGGELFDFL105 AEKESLTEDE 115 ATQFLKQILD125 GVHYLHSKRI135 AHFDLKPENI145 MLLDKNVPNP155 RIKLIDFGIA 165 HKIEGTPEFV184 APEIVNYEPL194 GLEADMWSIG204 VITYILLSGA214 SPFLGETKQE 224 TLTNISAVNY234 DFDEEYFSNT244 SELAKDFIRR254 LLVKDPKRRM264 IAQSLEHSWI 275 KAI
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| Ligand Name: L-serine-O-phosphate | Ligand Info | |||||
| Structure Description | Crystal structure of human ZIP kinase in complex with a tetracyclic pyridone inhibitor (Pyridone 6) | PDB:2J90 | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [1] |
| PDB Sequence |
FQSMVEDHYE
14 MGEELGSGQF24 AIVRKCRQKG34 TGKEYAAKFI44 KKRRLSSRRG55 VSREEIEREV 65 NILREIRHPN75 IITLHDIFEN85 KTDVVLILEL95 VSGGELFDFL105 AEKESLTEDE 115 ATQFLKQILD125 GVHYLHSKRI135 AHFDLKPENI145 MLLDKNVPNP155 RIKLIDFGIA 165 HKIEGTPEFV184 APEIVNYEPL194 GLEADMWSIG204 VITYILLSGA214 SPFLGETKQE 224 TLTNISAVNY234 DFDEEYFSNT244 SELAKDFIRR254 LLVKDPKRRM264 IAQSLEHSWI 275 KAI
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| Ligand Name: Phosphonothreonine | Ligand Info | |||||
| Structure Description | Crystal structure of human ZIP kinase in complex with a tetracyclic pyridone inhibitor (Pyridone 6) | PDB:2J90 | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [1] |
| PDB Sequence |
FQSMVEDHYE
14 MGEELGSGQF24 AIVRKCRQKG34 TGKEYAAKFI44 KKRRLSSRRG55 VSREEIEREV 65 NILREIRHPN75 IITLHDIFEN85 KTDVVLILEL95 VSGGELFDFL105 AEKESLTEDE 115 ATQFLKQILD125 GVHYLHSKRI135 AHFDLKPENI145 MLLDKNVPNP155 RIKLIDFGIA 165 HKIEGTPEFV184 APEIVNYEPL194 GLEADMWSIG204 VITYILLSGA214 SPFLGETKQE 224 TLTNISAVNY234 DFDEEYFSNT244 SELAKDFIRR254 LLVKDPKRRM264 IAQSLEHSWI 275 KAI
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TPO or .TPO2 or .TPO3 or :3TPO;style chemicals stick;color identity;select .A:200 or .A:263 or .A:264 or .A:266 or .A:267 or .A:268 or .A:269; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (4r)-7,8-Dichloro-1',9-Dimethyl-1-Oxo-1,2,4,9-Tetrahydrospiro[beta-Carboline-3,4'-Piperidine]-4-Carbonitrile | Ligand Info | |||||
| Structure Description | Crystal structure of human death associated protein kinase 3 (DAPK3) in complex with a beta-carboline ligand | PDB:3BHY | ||||
| Method | X-ray diffraction | Resolution | 1.24 Å | Mutation | No | [2] |
| PDB Sequence |
MVEDHYEMGE
17 ELGSGQFAIV27 RKCRQKGTGK37 EYAAKFIKKR47 RLSSSRRGVS57 REEIEREVNI 67 LREIRHPNII77 TLHDIFENKT87 DVVLILELVS97 GGELFDFLAE107 KESLTEDEAT 117 QFLKQILDGV127 HYLHSKRIAH137 FDLKPENIML147 LDKNVPNPRI157 KLIDFGIAHK 167 IEFGTPEFVA185 PEIVNYEPLG195 LEADMWSIGV205 ITYILLSGAS215 PFLGETKQET 225 LTNISAVNYD235 FDEEYFSNTS245 ELAKDFIRRL255 LVKDPKRRMT265 IAQSLEHSWI 275 KAIRRRNV
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7CP or .7CP2 or .7CP3 or :37CP;style chemicals stick;color identity;select .A:19 or .A:20 or .A:21 or .A:22 or .A:25 or .A:26 or .A:27 or .A:40 or .A:42 or .A:77 or .A:93 or .A:94 or .A:95 or .A:96 or .A:100 or .A:141 or .A:143 or .A:144 or .A:146 or .A:160 or .A:161; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LEU19
3.827
GLY20
3.130
SER21
4.017
GLY22
4.960
ALA25
3.902
ILE26
4.673
VAL27
2.977
ALA40
3.722
LYS42
3.939
ILE77
3.901
LEU93
3.844
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| Ligand Name: 5-(3-Sulfamoylphenyl)-1h-1,2,3,4-Tetrazol-1-Ide | Ligand Info | |||||
| Structure Description | Crystal structure of human death associated protein kinase 3 (DAPK3) in complex with compound 2 | PDB:5A6N | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | No | [3] |
| PDB Sequence |
MVEDHYEMGE
17 ELGSGQFAIV27 RKCRQKGTGK37 EYAAKFIKKR47 RLSSSRRGVS57 REEIEREVNI 67 LREIRHPNII77 TLHDIFENKT87 DVVLILELVS97 GGELFDFLAE107 KESLTEDEAT 117 QFLKQILDGV127 HYLHSKRIAH137 FDLKPENIML147 LDKNVPNPRI157 KLIDFGIAHK 167 IEAGNEFKNI177 FGTPEFVAPE187 IVNYEPLGLE197 ADMWSIGVIT207 YILLSGASPF 217 LGETKQETLT227 NISAVNYDFD237 EEYFSNTSEL247 AKDFIRRLLV257 KDPKRRMTIA 267 QSLEHSWIKA277 I
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .U7E or .U7E2 or .U7E3 or :3U7E;style chemicals stick;color identity;select .A:19 or .A:20 or .A:21 or .A:22 or .A:27 or .A:42 or .A:64 or .A:77 or .A:93 or .A:146 or .A:160 or .A:161 or .A:162; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-(6-{[(1r)-1-(Hydroxymethyl)propyl]amino}imidazo[1,2-B]pyridazin-3-Yl)benzoic Acid | Ligand Info | |||||
| Structure Description | Crystal structure of human death associated protein kinase 3 (DAPK3) in complex with an imidazo-pyridazine ligand | PDB:3BQR | ||||
| Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | No | [4] |
| PDB Sequence |
SMVEDHYEMG
16 EELGSGQFAI26 VRKCRQKGTG36 KEYAAKFIKK46 RRLSSSRRGV56 SREEIEREVN 66 ILREIRHPNI76 ITLHDIFENK86 TDVVLILELV96 SGGELFDFLA106 EKESLTEDEA 116 TQFLKQILDG126 VHYLHSKRIA136 HFDLKPENIM146 LLDKNVPNPR156 IKLIDFGIAH 166 KIEAGNNIFG179 TPEFVAPEIV189 NYEPLGLEAD199 MWSIGVITYI209 LLSGASPFLG 219 ETKQETLTNI229 SAVNYDFDEE239 YFSNTSELAK249 DFIRRLLVKD259 PKRRMTIAQS 269 LEHSWIKAIR279 RRNVR
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4RB or .4RB2 or .4RB3 or :34RB;style chemicals stick;color identity;select .A:19 or .A:20 or .A:21 or .A:27 or .A:40 or .A:42 or .A:64 or .A:77 or .A:93 or .A:94 or .A:95 or .A:96 or .A:100 or .A:143 or .A:146 or .A:160 or .A:161 or .A:162; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (2R)-2-{[1-(3-chlorophenyl)-4-oxo-4,5-dihydro-1H-pyrazolo[3,4-d]pyrimidin-6-yl]sulfanyl}propanamide | Ligand Info | |||||
| Structure Description | Crystal Structure of human zipper-interacting protein kinase (ZIPK, alias DAPK3) in complex with a pyrazolo[3,4-d]pyrimidinone ligand (HS38) | PDB:5VJA | ||||
| Method | X-ray diffraction | Resolution | 2.46 Å | Mutation | No | [5] |
| PDB Sequence |
SMVEDHYEMG
16 EELGSGQFAI26 VRKCRQKGTG36 KEYAAKFIKK46 RRRGVSREEI61 EREVNILREI 71 RHPNIITLHD81 IFENKTDVVL91 ILELVSGGEL101 FDFLAEKESL111 TEDEATQFLK 121 QILDGVHYLH131 SKRIAHFDLK141 PENIMLLDKN151 VPNPRIKLID161 FGIAHKIEAG 171 NEFKNIFGTP181 EFVAPEIVNY191 EPLGLEADMW201 SIGVITYILL211 SGASPFLGET 221 KQETLTNISA231 VNYDFDEEYF241 SNTSELAKDF251 IRRLLVKDPK261 RRMTIAQSLE 271 HSWIKA
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DUK or .DUK2 or .DUK3 or :3DUK;style chemicals stick;color identity;select .A:19 or .A:20 or .A:21 or .A:22 or .A:25 or .A:27 or .A:40 or .A:42 or .A:64 or .A:77 or .A:93 or .A:94 or .A:96 or .A:144 or .A:146 or .A:160 or .A:161 or .A:162; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Activation segment dimerization: a mechanism for kinase autophosphorylation of non-consensus sites. EMBO J. 2008 Feb 20;27(4):704-14. | ||||
| REF 2 | 7,8-dichloro-1-oxo-beta-carbolines as a versatile scaffold for the development of potent and selective kinase inhibitors with unusual binding modes. J Med Chem. 2012 Jan 12;55(1):403-13. | ||||
| REF 3 | De Novo Fragment Design for Drug Discovery and Chemical Biology. Angew Chem Int Ed Engl. 2015 Dec 7;54(50):15079-83. | ||||
| REF 4 | Crystal Structure of Human Death Associated Protein Kinase 3 (DAPK3) in Complex with an Imidazo-Pyridazine Ligand. | ||||
| REF 5 | Targeting Pim Kinases and DAPK3 to Control Hypertension. Cell Chem Biol. 2018 Oct 18;25(10):1195-1207.e32. | ||||
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