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Structure of PDB 6t8y Chain CCC Binding Site BS01

Receptor Information

>6t8y Chain CCC (length=373) Species: 759272 (Thermochaetoides thermophila DSM 1495)

ARLQMVKVLAVLYDGGEHAKQVPGLLGTTENELGLRKWLEDQGHTLVTTS
DKDREGSTFDRELEDAEIIITTPFHPGYLTAERLARAKKLKLAVTAGIGS
DHVDLDAANKTNGGITVAEVTGSNVVSVAEHVVMTILVLVRNFVPAHEQI
EAGRWDVAEVAKDEYDLEGKVVGTVGVGRIGERVLRRLKGFDCKELLYYD
YQPLSPEKEKEIGCRRVENLEEMLAQCDVVTINCPLHESTRGLFNKDLIS
KMKRGSWLVNTARGAIVVKEDVAEALRTGHLRGYGGDVWFPQPAPADHVL
RTAKNPFGGGNAMVPHMSGTSLDAQKRYAEGVKRILDSYLSGRFDYRPED
LIVHQGKYATRAYGQREDVKIPG

Ligand information

• Ligand ID: NAI
• InChI: InChI=1S/C21H29N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
• InChIKey: BOPGDPNILDQYTO-NNYOXOHSSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
  CACTVS 3.341: NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
  CACTVS 3.341: NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
• Formula: C21 H29 N7 O14 P2
• Name: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE;
  NADH
• ChEMBL: CHEMBL1234616
• DrugBank: DB00157
• ZINC: ZINC000008215403
• PDB chain: 6t8y Chain CCC Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6t8y Structural insights into the NAD + -dependent formate dehydrogenase mechanism revealed from the NADH complex and the formate NAD + ternary complex of the Chaetomium thermophilum enzyme.
• Resolution: 1.26 Å
• Binding residue (original residue number in PDB): I94 N120 V124 G172 G174 R175 I176 Y195 D196 Y197 Q198 C230 P231 H233 T257 A258 R259 D283 H312 S314 G315 A358
• Binding residue (residue number reindexed from 1): I98 N124 V128 G176 G178 R179 I180 Y199 D200 Y201 Q202 C234 P235 H237 T261 A262 R263 D287 H316 S318 G319 A362
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 1.17.1.9: formate dehydrogenase.

Gene Ontology

Molecular Function

• GO:0008863 formate dehydrogenase (NAD+) activity
• GO:0016491 oxidoreductase activity
• GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
• GO:0051287 NAD binding

Biological Process

• GO:0042183 formate catabolic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:6t8y, PDBe:6t8y, PDBj:6t8y
• PDBsum: 6t8y
• PubMed: 33148525
• UniProt: G0SGU4|FDH_CHATD Formate dehydrogenase (Gene Name=FDH)

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