Structure of PDB 1pj2 Chain D Binding Site BS01

Receptor Information
>1pj2 Chain D (length=553) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IKEKGKPLMLNPRTNKGMAFTLQERQMLGLQGLLPPKIETQDIQALRFHR
NLKKMTSPLEKYIYIMGIQERNEKLFYRILQDDIESLMPIVYTPTVGLAC
SQYGHIFRRPKGLFISISDRGHVRSIVDNWPENHVKAVVVTDGERILGLG
DLGVYGMGIPVGKLCLYTACAGIRPDRCLPVCIDVGTDNIALLKDPFYMG
LYQKRDRTQQYDDLIDEFMKAITDRYGRNTLIQFEDFGNHNAFRFLRKYR
EKYCTFNDDIQGTAAVALAGLLAAQKVISKPISEHKILFLGAGEAALGIA
NLIVMSMVENGLSEQEAQKKIWMFDKYGLLVKGRKAKIDSYQEPFTHSAP
ESIPDTFEDAVNILKPSTIIGVAGAGRLFTPDVIRAMASINERPVIFALS
NPTAQAECTAEEAYTLTEGRCLFASGSPFGPVKLTDGRVFTPGQGNNVYI
FPGVALAVILCNTRHISDSVFLEAAKALTSQLTDEELAQGRLYPPLANIQ
EVSINIAIKVTEYLYANKMAFRYPEPEDKAKYVKERTWRSEYDSLLPDVY
EWP
Ligand information
Ligand IDNAI
InChIInChI=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
InChIKeyBOPGDPNILDQYTO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(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 3.341NC(=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 1.5.0c1nc(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 3.341NC(=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
FormulaC21 H29 N7 O14 P2
Name1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE;
NADH
ChEMBLCHEMBL1234616
DrugBankDB00157
ZINCZINC000008215403
PDB chain1pj2 Chain A Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1pj2 Crystal structures of substrate complexes of malic enzyme and insights into the catalytic mechanism.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		D3244 R3245
Binding residue
(residue number reindexed from 1)		D224 R225
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) Y3112 R3165 K3183 E3255 D3256 D3278 D3279 N3421
Catalytic site (residue number reindexed from 1) Y92 R145 K163 E235 D236 D258 D259 N401
Enzyme Commision number 1.1.1.38: malate dehydrogenase (oxaloacetate-decarboxylating).
Gene Ontology
Molecular Function
GO:0004470 malic enzyme activity
GO:0004471 malate dehydrogenase (decarboxylating) (NAD+) activity
GO:0004473 malate dehydrogenase (decarboxylating) (NADP+) activity
GO:0008948 oxaloacetate decarboxylase activity
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0046872 metal ion binding
GO:0051287 NAD binding
Biological Process
GO:0006090 pyruvate metabolic process
GO:0006108 malate metabolic process
GO:1902031 regulation of NADP metabolic process
Cellular Component
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0043231 intracellular membrane-bounded organelle

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1pj2, PDBe:1pj2, PDBj:1pj2
PDBsum1pj2
PubMed12962632
UniProtP23368|MAOM_HUMAN NAD-dependent malic enzyme, mitochondrial (Gene Name=ME2)

[Back to BioLiP]