Structure of PDB 1p9l Chain B Binding Site BS01

Receptor Information
>1p9l Chain B (length=245) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRVGVLGAKGKVGTTMVRAVAAADDLTLSAELDAGDPLSLLTDGNTEVVI
DFTHPDVVMGNLEFLIDNGIHAVVGTTGFTAERFQQVESWLVAKPNTSVL
IAPNFAIGAVLSMHFAKQAARFFDSAEVIELHHPHKADAPSGTAARTAKL
IAEARKGLPPNPDATSTSLPGARGADVDGIPVHAVRLAGLVAHQEVLFGT
EGETLTIRHDSLDRTSFVPGVLLAVRRIAERPGLTVGLEPLLDLH
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 chain1p9l Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1p9l The three-dimensional structures of the Mycobacterium tuberculosis dihydrodipicolinate reductase-NADH-2,6-PDC and -NADPH-2,6-PDC complexes. Structural and mutagenic analysis of relaxed nucleotide specificity.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		G7 G10 K11 V12 D33 A34 F52 T53 V57 G75 T76 T77 P103 N104 F105 F217
Binding residue
(residue number reindexed from 1)		G7 G10 K11 V12 D33 A34 F52 T53 V57 G75 T76 T77 P103 N104 F105 F217
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) H132 K136
Catalytic site (residue number reindexed from 1) H132 K136
Enzyme Commision number 1.17.1.8: 4-hydroxy-tetrahydrodipicolinate reductase.
Gene Ontology
Molecular Function
GO:0008839 4-hydroxy-tetrahydrodipicolinate reductase
GO:0016491 oxidoreductase activity
GO:0016726 oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor
GO:0050661 NADP binding
GO:0051287 NAD binding
GO:0070402 NADPH binding
GO:0070404 NADH binding
Biological Process
GO:0009085 lysine biosynthetic process
GO:0009089 lysine biosynthetic process via diaminopimelate
GO:0019877 diaminopimelate biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0009274 peptidoglycan-based cell wall

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1p9l, PDBe:1p9l, PDBj:1p9l
PDBsum1p9l
PubMed12962488
UniProtP9WP23|DAPB_MYCTU 4-hydroxy-tetrahydrodipicolinate reductase (Gene Name=dapB)

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