Structure of PDB 4fpb Chain B Binding Site BS04

Receptor Information

>4fpb Chain B (length=899) Species: 9606 (Homo sapiens)

DDQVKKIDKYLYAMRLSDETLIDIMTRFRKEMKNGLSRDFNPTATVKMLP
TFVRSIPDGSEKGDFIALDLGGSSFRILRVQVNHEKNQNVHMESEVYDTP
ENIVHGSGSQLFDHVAECLGDFMEKRKIKDKKLPVGFTFSFPCQQSKIDE
AILITWTKRFKASGVEGADVVKLLNKAIKKRGDYDANIVAVVNDTVGTMM
TCGYDDQHCEVGLIIGTGTNACYMEELRHIDLVEGDEGRMCINTEWGAFG
DDGSLEDIRTEFDREIDRGSLNPGKQLFEKMVSGMYLGELVRLILVKMAK
EGLLFEGRITPELLTRGKFNTSDVSAIEKNKEGLHNAKEILTRLGVEPSD
DDCVSVQHVCTIVSFRSANLVAATLGAILNRLRDNKGTPRLRTTVGVDGS
LYKTHPQYSRRFHKTLRRLVPDSDVRFLLSESGSGKGAAMVTAVAYRLAE
QHRQIEETLAHFHLTKDMLLEVKKRMRAEMELGLRKQTHNNAVVKMLPSF
VRRTPDGTENGDFLALDLGGTNFRVLLVKIRSGKKRTVEMHNKIYAIPIE
IMQGTGEELFDHIVSCISDFLDYMGIKGPRMPLGFTFSFPCQQTSLDAGI
LITWTKGFKATDCVGHDVVTLLRDAIKRREEFDLDVVAVVNDTVGTMMTC
AYEEPTCEVGLIVGTGSNACYMEEMKNVEMVEGDQGQMCINMEWGAFGDN
GCLDDIRTHYDRLVDEYSLNAGKQRYEKMISGMYLGEIVRNILIDFTKKG
FLFRGQISETLKTRGIFETKFLSQIESDRLALLQVRAILQQLGLNSTCDD
SILVKTVCGVVSRRAAQLCGAGMAAVVDKIRENRGLDRLNVTVGVDGTLY
KLHPHFSRIMHQTVKELSPKCNVSFLLSEDGSGKGAALITAVGVRLRTE

Ligand information

• Ligand ID: 0WK
• InChI: InChI=1S/C6H13O8P/c7-3-1-13-4(6(9)5(3)8)2-14-15(10,11)12/h3-9H,1-2H2,(H2,10,11,12)/t3-,4+,5+,6+/m0/s1
• InChIKey: KAJAXXUCVJFKFM-SLPGGIOYSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: C1C(C(C(C(O1)COP(=O)(O)O)O)O)O
  CACTVS 3.370: O[C@H]1CO[C@H](CO[P](O)(O)=O)[C@@H](O)[C@@H]1O
  ACDLabs 12.01: O=P(O)(O)OCC1OCC(O)C(O)C1O
  OpenEye OEToolkits 1.7.6: C1[C@@H]([C@H]([C@@H]([C@H](O1)COP(=O)(O)O)O)O)O
  CACTVS 3.370: O[CH]1CO[CH](CO[P](O)(O)=O)[CH](O)[CH]1O
• Formula: C6 H13 O8 P
• Name: 1,5-anhydro-6-O-phosphono-D-glucitol
• PDB chain: 4fpb Chain B Residue 1004

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4fpb Inhibitor Sites of Unequal Affinity Linked by Binding Synergism in Mutant Forms of Recombinant Human Hexokinase Type-I
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): D532 T536 D657 G679 T680 G862 T863 G896 S897
• Binding residue (residue number reindexed from 1): D517 T521 D642 G664 T665 G847 T848 G881 S882
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): R539 S603 T618 D657
• Catalytic site (residue number reindexed from 1): R524 S588 T603 D642
• Enzyme Commision number: 2.7.1.1: hexokinase.

Gene Ontology

Molecular Function

• GO:0004340 glucokinase activity
• GO:0004396 hexokinase activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0005536 D-glucose binding
• GO:0008865 fructokinase activity
• GO:0016301 kinase activity
• GO:0016773 phosphotransferase activity, alcohol group as acceptor
• GO:0019158 mannokinase activity
• GO:0042834 peptidoglycan binding
• GO:0047931 glucosamine kinase activity

Biological Process

• GO:0001678 intracellular glucose homeostasis
• GO:0002720 positive regulation of cytokine production involved in immune response
• GO:0005975 carbohydrate metabolic process
• GO:0006002 fructose 6-phosphate metabolic process
• GO:0006006 glucose metabolic process
• GO:0006013 mannose metabolic process
• GO:0006096 glycolytic process
• GO:0006954 inflammatory response
• GO:0009298 GDP-mannose biosynthetic process
• GO:0016310 phosphorylation
• GO:0019318 hexose metabolic process
• GO:0032731 positive regulation of interleukin-1 beta production
• GO:0045087 innate immune response
• GO:0046835 carbohydrate phosphorylation
• GO:0051156 glucose 6-phosphate metabolic process
• GO:0061621 canonical glycolysis
• GO:0061728 GDP-mannose biosynthetic process from mannose
• GO:0072655 establishment of protein localization to mitochondrion
• GO:0072656 maintenance of protein location in mitochondrion
• GO:0141199 GDP-mannose biosynthetic process from glucose
• GO:1901135 carbohydrate derivative metabolic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005741 mitochondrial outer membrane
• GO:0005829 cytosol
• GO:0045121 membrane raft

External links

• PDB: RCSB:4fpb, PDBe:4fpb, PDBj:4fpb
• PDBsum: 4fpb
• UniProt: P19367|HXK1_HUMAN Hexokinase-1 (Gene Name=HK1)