Structure of PDB 5n5s Chain D Binding Site BS01

Receptor Information

>5n5s Chain D (length=480) Species: 3218 (Physcomitrium patens)

TPKKYNIFLASKPVDGDRKWLDVTNKYTNDVAAKVPQATHKDIDDAIDAA
VAAAPAMAAMGAYERKAVLEKVVAELKNRFEEIAQTLTMESGKPIKDARG
EVTRTIDTFQVAAEESVRIYGEHIPLDISARNKGLQGIVKKFPIGPVSMV
SPWNFPLNLVAHKVAPAIAVGCPFVLKPASRTPLSALILGEILHKIEELP
LGAFSILPVSREDADMFTVDERFKLLTFTGSGPIGWDMKARAGKKKVVME
LGGNAPCIVDDYVPDLDYTIQRLINGGFYQGGQSCIHMQRLYVHERLYDE
VKEGFVAAVKKLKMGNPFEEDTYLGPMISESAAKGIEDWVKEAVAKGGKL
LTGGNRKGAFIEPTVIEDVPIEANARKEEIFGPVVLLYKYSDFKEAVKEC
NNTHYGLQSGIFTKDLNKAFYAFEHMEVGGVILNDSPALRVDSQPYGGLK
DSGIQREGVKYAMDDMLETKVLVMRNVGTL

Ligand information

• Ligand ID: NAP
• InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
• InChIKey: XJLXINKUBYWONI-NNYOXOHSSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
  CACTVS 3.341: NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
  CACTVS 3.341: NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
  OpenEye OEToolkits 1.5.0: c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
• Formula: C21 H28 N7 O17 P3
• Name: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE;
  2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
• ChEMBL: CHEMBL295069
• DrugBank: DB03461
• PDB chain: 5n5s Chain D Residue 503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5n5s The ALDH21 gene found in lower plants and some vascular plants codes for a NADP(+) -dependent succinic semialdehyde dehydrogenase.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): V167 S168 P169 W170 N171 L176 K194 S197 R228 A231 T246 G247 S248 I251 E267 L268 C302 E396 F398 Y463
• Binding residue (residue number reindexed from 1): V150 S151 P152 W153 N154 L159 K177 S180 R211 A214 T229 G230 S231 I234 E250 L251 C285 E379 F381 Y446
• Annotation score: 3
• Binding affinity: MOAD: Kd=31uM

Enzymatic activity

• Catalytic site (original residue number in PDB): N171 K194 E267 C302 E396 E474
• Catalytic site (residue number reindexed from 1): N154 K177 E250 C285 E379 E457
• Enzyme Commision number: 1.2.1.9: glyceraldehyde-3-phosphate dehydrogenase (NADP(+)).

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0008911 lactaldehyde dehydrogenase (NAD+) activity
• GO:0016491 oxidoreductase activity
• GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor

External links

• PDB: RCSB:5n5s, PDBe:5n5s, PDBj:5n5s
• PDBsum: 5n5s
• PubMed: 28749584
• UniProt: A9SS48