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Structure of PDB 2dkn Chain A Binding Site BS01

Receptor Information

>2dkn Chain A (length=254) Species: 402890 (Pseudomonas sp. B-0831)

SVIAITGSASGIGAALKELLARAGHTVIGIDRGQADIEADLSTPGGRETA
VAAVLDRCGGVLDGLVCCAGVGVTAANSGLVVAVNYFGVSALLDGLAEAL
SRGQQPAAVIVGSIAATQPGAAELPMVEAMLAGDEARAIELAEQQGQTHL
AYAGSKYAVTCLARRNVVDWAGRGVRLNVVAPGAVETPLLQASKADPRYG
ESTRRFVAPLGRGSEPREVAEAIAFLLGPQASFIHGSVLFVDGGMDALMR
AKTF

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: 2dkn Chain A Residue 4000

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2dkn Apo- and Holo-structures of 3{alpha}-Hydroxysteroid Dehydrogenase from Pseudomonas sp. B-0831: LOOP-HELIX TRANSITION INDUCED BY COENZYME BINDING
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): G8 S11 G12 I13 D32 R33 A40 L42 C69 A70 G71 V72 V85 V112 S114 Y153 K157 P183 G184 A185 V186 T188 L190
• Binding residue (residue number reindexed from 1): G7 S10 G11 I12 D31 R32 A39 L41 C68 A69 G70 V71 V84 V111 S113 Y152 K156 P182 G183 A184 V185 T187 L189
• Annotation score: 4
• Binding affinity: MOAD: Kd=8.8uM

Enzymatic activity

• Catalytic site (original residue number in PDB): G12
• Catalytic site (residue number reindexed from 1): G11
• Enzyme Commision number: 1.1.1.50: 3alpha-hydroxysteroid 3-dehydrogenase (Si-specific).

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0016491 oxidoreductase activity
• GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
• GO:0047042 androsterone dehydrogenase (B-specific) activity

External links

• PDB: RCSB:2dkn, PDBe:2dkn, PDBj:2dkn
• PDBsum: 2dkn
• PubMed: 16905772
• UniProt: Q59718

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