Structure of PDB 3d7k Chain B Binding Site BS03

Receptor Information

>3d7k Chain B (length=554) Species: 294 (Pseudomonas fluorescens)

AMITGGELVVRTLIKAGVEHLFGLHGAHIDTIFQACLDHDVPIIDTRHEA
AAGHAAEGYARAGAKLGVALVTAGGGFTNAVTPIANAWLDRTPVLFLTGS
GALRDDETNTLQAGIDQVAMAAPITKWAHRVMATEHIPRLVMQAIRAALS
APRGPVLLDLPWDILMNQIDEDSVIIPDLVLSAHGARPDPADLDQALALL
RKAERPVIVLGSEASRTARKTALSAFVAATGVPVFADYEGLSMLSGLPDA
MRGGLVQNLYSFAKADAAPDLVLMLGARFGLNTGHGSGQLIPHSAQVIQV
DPDACELGRLQGIALGIVADVGGTIEALAQATAQDAAWPDRGDWCAKVTD
LAQERYASIAAKSSSEHALHPFHASQVIAKHVDAGVTVVADGALTYLWLS
EVMSRVKPGGFLCHGYLGSMGVGFGTALGAQVADLEAGRRTILVTGDGSV
GYSIGEFDTLVRKQLPLIVIIMNNQSWGATLHFQQLAVGPNRVTGTRLEN
GSYHGVAAAFGADGYHVDSVESFSAALAQALAHNRPACINVAVALDPIPP
EELI

Ligand information

• Ligand ID: D7K
• InChI: InChI=1S/C20H27N4O11P3S/c1-13-17(9-10-34-38(31,32)35-37(28,29)30)39-19(24(13)12-15-11-22-14(2)23-18(15)21)20(25,36(26,27)33-3)16-7-5-4-6-8-16/h4-8,11,25H,9-10,12H2,1-3H3,(H5-,21,22,23,26,27,28,29,30,31,32)/p+1/t20-/m0/s1
• InChIKey: NEEQBMRCDKRNBV-FQEVSTJZSA-O
• SMILES:
  ACDLabs 10.04: O=P(O)(OP(=O)(O)O)OCCc1sc([n+](c1C)Cc2cnc(nc2N)C)C(O)(c3ccccc3)P(=O)(OC)O
  OpenEye OEToolkits 1.5.0: Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(c3ccccc3)(O)P(=O)(O)OC)CCOP(=O)(O)OP(=O)(O)O
  OpenEye OEToolkits 1.5.0: Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@](c3ccccc3)(O)[P@@](=O)(O)OC)CCO[P@@](=O)(O)OP(=O)(O)O
  CACTVS 3.341: CO[P](O)(=O)[C](O)(c1ccccc1)c2sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)[n+]2Cc3cnc(C)nc3N
  CACTVS 3.341: CO[P@@](O)(=O)[C@@](O)(c1ccccc1)c2sc(CCO[P@](O)(=O)O[P](O)(O)=O)c(C)[n+]2Cc3cnc(C)nc3N
• Formula: C20 H28 N4 O11 P3 S
• Name: 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(S)-hydroxy[(R)-hydroxy(methoxy)phosphoryl]phenylmethyl}-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium
• ZINC: ZINC000058661176
• PDB chain: 3d7k Chain B Residue 572

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3d7k Probing the active center of benzaldehyde lyase with substitutions and the pseudosubstrate analogue benzoylphosphonic acid methyl ester
• Resolution: 2.49 Å
• Binding residue (original residue number in PDB): G393 A394 L395 T396 G419 M421 G447 D448 G449 S450 Y453 N475 S477 W478 G479 A480 T481
• Binding residue (residue number reindexed from 1): G392 A393 L394 T395 G418 M420 G446 D447 G448 S449 Y452 N474 S476 W477 G478 A479 T480
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=4.60,Kd=25uM

Enzymatic activity

• Catalytic site (original residue number in PDB): L25 G27 A28 H29 I30 E50 T73 L112 Q113 A114 G115 W163 L256 T284 G393 G419 M421 D448 N475 S477 W478 A480 T481 F484 L546
• Catalytic site (residue number reindexed from 1): L24 G26 A27 H28 I29 E49 T72 L111 Q112 A113 G114 W162 L255 T283 G392 G418 M420 D447 N474 S476 W477 A479 T480 F483 L545
• Enzyme Commision number: 4.1.2.38: benzoin aldolase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003824 catalytic activity
• GO:0003984 acetolactate synthase activity
• GO:0016829 lyase activity
• GO:0030976 thiamine pyrophosphate binding
• GO:0046872 metal ion binding
• GO:0050660 flavin adenine dinucleotide binding

Biological Process

• GO:0009097 isoleucine biosynthetic process
• GO:0009099 L-valine biosynthetic process
• GO:0019752 carboxylic acid metabolic process

Cellular Component

• GO:0005948 acetolactate synthase complex

External links

• PDB: RCSB:3d7k, PDBe:3d7k, PDBj:3d7k
• PDBsum: 3d7k
• PubMed: 18570438
• UniProt: Q9F4L3