Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T76414 | Target Info | |||
| Target Name | Glutamate receptor ionotropic NMDA 2B (NMDAR2B) | ||||
| Synonyms | NR3; NR2B; NMDA receptor subunit 2B; NMDA receptor NR2B; NMDA NR2B receptor; N-methylD-aspartate receptor subtype 2B; N-methyl-D-aspartate receptor subunit 3; N-methyl D-aspartate receptor subtype 2B; HNR3; Glutamate receptor ionotropic, NMDA 2B; Glutamate receptor NR2B subunit; Glutamate [NMDA] receptor subunit epsilon-2; GluN2B | ||||
| Target Type | Successful Target | ||||
| Gene Name | GRIN2B | ||||
| Biochemical Class | Glutamate-gated ion channel | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Adenosine triphosphate | Ligand Info | |||||
| Structure Description | Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B(S1303D) | PDB:7KL1 | ||||
| Method | X-ray diffraction | Resolution | 2.40 Å | Mutation | Yes | [1] |
| PDB Sequence |
RNKLRRQHDY
1304 DTFVD
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| Ligand Name: Esketamine | Ligand Info | |||||
| Structure Description | Structure of the human GluN1-GluN2B NMDA receptor in complex with S-ketamine,glycine and glutamate | PDB:7EU8 | ||||
| Method | Electron microscopy | Resolution | 4.07 Å | Mutation | No | [2] |
| PDB Sequence |
SIGIAVILVS
45 DEVAIKDAHE55 KDDFHHLSVV65 PRVELVAMNE75 TDPKSIITRI85 CDLMSDRKIQ 95 GVVFADDTDQ105 EAIAQILDFI115 SAQTLTPILG125 IHGGSSMIMA135 DKDESSMFFQ 145 FGPSIEQQAS155 VMLNIMEEYD165 WYIFSIVTTY175 FPGYQDFVNK185 IRSTIENSFV 195 GWELEDSKIQ217 NQLKKLQSPI227 ILLYCTKEEA237 TYIFEVANSV247 GLTGYGYTWI 257 VPSLVAGDTD267 TVPAEFPTGL277 ISVSYDEWDY287 GLPARVRDGI297 AIITTAASDM 307 LSEHSFIPEP317 KSSCYNTHEK327 QSNMLNRYLI340 NVTFEGRNLS350 FSEDGYQMHP 360 KLVIILLNKE370 RKWERVGKWK380 DKSLQMKYYV390 WPDDHLSIVT410 LEEAPFVIVE 420 SVDPLSGTCM430 RNTVPCQKRI440 VGYIKKCCKG459 FCIDILKKIS469 KSVKFTYDLY 479 LVTNGKHGKK489 INGTWNGMIG499 EVVMKRAYMA509 VGSLTINEER519 SEVVDFSVPF 529 IETGISVMVS539 RSNGTVSPSA549 FLEPFSADVW559 VMMFVMLLIV569 SAVAVFVFEY 579 FTIGKAIWLL609 WGLVFNNSVP619 VQNPKGTTSK629 IMVSVWAFFA639 VIFLASYTAN 649 LAAFMIQEEY659 VDQVSGLSDK669 KFQRPNDFSP679 PFRFGTVPNG689 STERNIRNNY 699 AEMHAYMGKF709 NQRGVDDALL719 SLKTGKLDAF729 IYDAAVLNYM739 AGRDEGCKLV 749 TIGSGKVFAS759 TGYGIAIQKD769 SGWKRQVDLA779 ILQLFGDGEM789 EELEALWLTG 799 ICHNSSQLDI815 DNMAGVFYML825 GAAMALSLIT835 FIC
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| Ligand Name: adenosine diphosphate | Ligand Info | |||||
| Structure Description | Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B | PDB:7UJP | ||||
| Method | X-ray diffraction | Resolution | 2.56 Å | Mutation | Yes | [1] |
| PDB Sequence |
RNKLRRQHSY
1304 DTFV
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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 .ADP or .ADP2 or .ADP3 or :3ADP;style chemicals stick;color identity;select .C:1302; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: EVT-101 free base | Ligand Info | |||||
| Structure Description | CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN COMPLEX WITH EVT-101 | PDB:5EWM | ||||
| Method | X-ray diffraction | Resolution | 2.76 Å | Mutation | Yes | [3] |
| PDB Sequence |
PPSIGIAVIL
41 VGTSDEVAIK51 DFHHLSVVPR67 VELVAMNETD77 PKSIITRICD87 LMSDRKIQGV 97 VFADDTDQEA107 IAQILDFISA117 QTLTPILGIH127 GGSSMIMADK137 DESSMFFQFG 147 PSIEQQASVM157 LNIMEEYDWY167 IFSIVTTYFP177 GYQDFVNKIR187 STIENSFVGW 197 ELEEVLLLDM207 SLDDGDSKIQ217 NQLKKLQSPI227 ILLYCTKEEA237 TYIFEVANSV 247 GLTGYGYTWI257 VPSLVAGDTD267 TVPAEFPTGL277 ISVSYDEWDY287 GLPARVRDGI 297 AIITTAASDM307 LSEHSFIPEP317 KSSCYNTHEK327 RIYQSNMLNR337 YLINVTFEGR 347 DLSFSEDGYQ357 MHPKLVIILL367 NKERKWERVG377 KWKDKSLQMK387 YYVWPR |
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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 .5SM or .5SM2 or .5SM3 or :35SM;style chemicals stick;color identity;select .B:78 or .B:82 or .B:110 or .B:111 or .B:113 or .B:114 or .B:134 or .B:135 or .B:136 or .B:137 or .B:177; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol | Ligand Info | |||||
| Structure Description | CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN COMPLEX WITH IFENPRODIL | PDB:5EWJ | ||||
| Method | X-ray diffraction | Resolution | 2.77 Å | Mutation | Yes | [3] |
| PDB Sequence |
PPSIGIAVIL
41 VGTSDEVAIK51 DLSVVPRVEL70 VAMNETDPKS80 IITRICDLMS90 DRKIQGVVFA 100 DDTDQEAIAQ110 ILDFISAQTL120 TPILGIHGGS130 SMIMADKDES140 SMFFQFGPSI 150 EQQASVMLNI160 MEEYDWYIFS170 IVTTYFPGYQ180 DFVNKIRSTI190 ENSFVGWELE 200 EVLLLDMSLD210 DGDSKIQNQL220 KKLQSPIILL230 YCTKEEATYI240 FEVANSVGLT 250 GYGYTWIVPS260 LVAGDTDTVP270 AEFPTGLISV280 SYDEWDYGLP290 ARVRDGIAII 300 TTAASDMLSE310 HSFIPEPKSS320 CYNTHEKRIY330 QSNMLNRYLI340 NVTFEGRDLS 350 FSEDGYQMHP360 KLVIILLNKE370 RKWERVGKWK380 DKSLQMKYYV390 WPR |
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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 .QEL or .QEL2 or .QEL3 or :3QEL;style chemicals stick;color identity;select .B:78 or .B:82 or .B:107 or .B:110 or .B:111 or .B:114 or .B:174 or .B:175 or .B:176 or .B:177 or .B:207 or .B:233 or .B:236; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: NMDA receptor antagonist 2 | Ligand Info | |||||
| Structure Description | CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN COMPLEX WITH MK-22 | PDB:5EWL | ||||
| Method | X-ray diffraction | Resolution | 2.98 Å | Mutation | Yes | [3] |
| PDB Sequence |
PPSIGIAVIL
41 VGTSDEVAIK51 DLSVVPRVEL70 VAMNETDPKS80 IITRICDLMS90 DRKIQGVVFA 100 DDTDQEAIAQ110 ILDFISAQTL120 TPILGIHGGS130 SMIMADKDES140 SMFFQFGPSI 150 EQQASVMLNI160 MEEYDWYIFS170 IVTTYFPGYQ180 DFVNKIRSTI190 ENSFVGWELE 200 EVLLLDMSLD210 DGDSKIQNQL220 KKLQSPIILL230 YCTKEEATYI240 FEVANSVGLT 250 GYGYTWIVPS260 LVAGDTDTVP270 AEFPTGLISV280 SYDEWDYGLP290 ARVRDGIAII 300 TTAASDMLSE310 HSFIPEPKSS320 CYNTHEKRIY330 QSNMLNRYLI340 NVTFEGRDLS 350 FSEDGYQMHP360 KLVIILLNKE370 RKWERVGKWK380 DKSLQMKYYV390 WP |
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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 .5SL or .5SL2 or .5SL3 or :35SL;style chemicals stick;color identity;select .B:78 or .B:82 or .B:106 or .B:107 or .B:110 or .B:111 or .B:114 or .B:135 or .B:174 or .B:175 or .B:176 or .B:177 or .B:233 or .B:236; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | CaMKII binds both substrates and activators at the active site. Cell Rep. 2022 Jul 12;40(2):111064. | ||||
| REF 2 | Structural basis of ketamine action on human NMDA receptors. Nature. 2021 Aug;596(7871):301-305. | ||||
| REF 3 | A Novel Binding Mode Reveals Two Distinct Classes of NMDA Receptor GluN2B-selective Antagonists. Mol Pharmacol. 2016 May;89(5):541-51. | ||||
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