Structure of PDB 3kq4 Chain A Binding Site BS01

Receptor Information
>3kq4 Chain A (length=385) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SCSVPSAQEPLVNGIQVLMENSVTSSAYPNPSILIAMNLAGAYNLKAQKL
LTYQLMSSDNNDLTIGHLGLTIMALTSSCRDPGDKVSILQRQMENWAPSS
PNAEASAFYGPSLAILALCQKNSEATLPIAVRFAKTLLANSSPFNVDTGA
MATLALTCMYNKIPVGSEEGYRSLFGQVLKDIVEKISMKIKDNGIIGDIY
STGLAMQALSVTPEPSKKEWNCKKTTDMILNEIKQGKFHNPMSIAQILPS
LKGKTYLDVPQVTCSPDHEVQPTLPSASNITVIYTINNQLRGVELLFNET
INVSVKSGSVLLVVLEEAQRKNPMFKFETTMTSWGLVVSSINNIAENVNH
KTYWQFLSGVTPLNEGVADYIPFNHEHITANFTQY
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 chain3kq4 Chain A Residue 2007 [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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PDB3kq4 Structural basis for receptor recognition of vitamin-B(12)-intrinsic factor complexes.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		G90 H91 S130 Y133 D171 Y224 S225 S365 W366 G367 V369 V370 W386 F388 L395 N396 E397 G398 Y417
Binding residue
(residue number reindexed from 1)		G66 H67 S106 Y109 D147 Y200 S201 S333 W334 G335 V337 V338 W354 F356 L363 N364 E365 G366 Y385
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0031419 cobalamin binding
GO:0140355 cargo receptor ligand activity
Biological Process
GO:0006824 cobalt ion transport
GO:0015889 cobalamin transport
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005768 endosome
GO:0005902 microvillus
GO:0016324 apical plasma membrane
GO:0043202 lysosomal lumen

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3kq4, PDBe:3kq4, PDBj:3kq4
PDBsum3kq4
PubMed20237569
UniProtP27352|IF_HUMAN Cobalamin binding intrinsic factor (Gene Name=CBLIF)

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