Structure of PDB 3som Chain M Binding Site BS01

Receptor Information
>3som Chain M (length=231) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EPKVAELKQKIEDTLCPFGFEVYPFQVAWYNELLPPAFHLPLPGPTLAFL
VLSTPAMFDRALKPFLQSCHLRMLTDPVDQCVAYHLGRVRESLPELQIEI
IADYEVHPNRRPKILAQTAAHVAGAAYYYQRQDVEADPWGNQRISGVCIH
PRFGGWFAIRGVVLLPGIEVPDLPPRKPHDCVPTRADRIALLEGFNFHWR
DWTYRDAVTPQERYSEEQKAYFSTPPAQRLA
Ligand information
Ligand IDB12
InChIInChI=1S/C62H90N13O14P.Co/c1-29-20-39-40(21-30(29)2)75(28-70-39)57-52(84)53(41(27-76)87-57)89-90(85,86)88-31(3)26-69-49(83)18-19-59(8)37(22-46(66)80)56-62(11)61(10,25-48(68)82)36(14-17-45(65)79)51(74-62)33(5)55-60(9,24-47(67)81)34(12-15-43(63)77)38(71-55)23-42-58(6,7)35(13-16-44(64)78)50(72-42)32(4)54(59)73-56;/h20-21,23,28,31,34-37,41,52-53,56-57,72,76,84H,12-19,22,24-27H2,1-11H3,(H2,63,77)(H2,64,78)(H2,65,79)(H2,66,80)(H2,67,81)(H2,68,82)(H,69,83)(H,85,86);/q;+2/b42-23-,50-32-,55-33-;/t31-,34-,35-,36-,37+,41-,52-,53-,56-,57+,59-,60+,61+,62+;/m1./s1
InChIKeyLKVIQTCSMMVGFU-DWSMJLPVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)n(cn2)C3C(C(C(O3)CO)OP(=O)(O)OC(C)CNC(=O)CCC4(C(C5C6(C(C(C7=[N]6[Co+2]89[N]5=C4C(=C1[NH]8C(=CC2=[N]9C(=C7C)C(C2CCC(=O)N)(C)CC(=O)N)C(C1CCC(=O)N)(C)C)C)CCC(=O)N)(C)CC(=O)N)C)CC(=O)N)C)O
CACTVS 3.370[Co++]|1|2|3|N4C5=CC6=N|1C(=C(C)C7=N|2[C](C)([CH]8N|3=C(C(=C4[CH](CCC(N)=O)C5(C)C)C)[C](C)(CCC(=O)NC[CH](C)O[P](O)(=O)O[CH]9[CH](O)[CH](O[CH]9CO)n%10cnc%11cc(C)c(C)cc%10%11)[CH]8CC(N)=O)[C](C)(CC(N)=O)[CH]7CCC(N)=O)[C](C)(CC(N)=O)[CH]6CCC(N)=O
CACTVS 3.370[Co++]|1|2|3|N4C5=CC6=N|1C(=C(C)C7=N|2[C@@](C)([C@@H]8N|3=C(C(=C4[C@@H](CCC(N)=O)C5(C)C)C)[C@](C)(CCC(=O)NC[C@@H](C)O[P](O)(=O)O[C@H]9[C@@H](O)[C@H](O[C@@H]9CO)n%10cnc%11cc(C)c(C)cc%10%11)[C@H]8CC(N)=O)[C@@](C)(CC(N)=O)[C@@H]7CCC(N)=O)[C@@](C)(CC(N)=O)[C@@H]6CCC(N)=O
FormulaC62 H89 Co N13 O14 P
NameCOBALAMIN
ChEMBL
DrugBank
ZINC
PDB chain3som Chain M Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3som Structure of MMACHC reveals an arginine-rich pocket and a domain-swapped dimer for its B12 processing function.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		L34 L35 P36 D104 A117 Q118 H122 Y129 Q131 R144 S146 C149 I160 F196 W200
Binding residue
(residue number reindexed from 1)		L33 L34 P35 D103 A116 Q117 H121 Y128 Q130 R143 S145 C148 I159 F195 W199
Annotation score2
Enzymatic activity
Enzyme Commision number 1.16.1.6: cyanocobalamin reductase.
2.5.1.151: alkylcobalamin dealkylase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0016740 transferase activity
GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
GO:0031419 cobalamin binding
GO:0032451 demethylase activity
GO:0033787 cyanocobalamin reductase (cyanide-eliminating) (NADP+) activity
GO:0042803 protein homodimerization activity
GO:0043295 glutathione binding
GO:0071949 FAD binding
Biological Process
GO:0006749 glutathione metabolic process
GO:0009235 cobalamin metabolic process
GO:0070988 demethylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3som, PDBe:3som, PDBj:3som
PDBsum3som
PubMed22642810
UniProtQ9Y4U1|MMAC_HUMAN Cyanocobalamin reductase / alkylcobalamin dealkylase (Gene Name=MMACHC)

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