Structure of PDB 2pmv Chain C Binding Site BS01

Receptor Information
>2pmv Chain C (length=378) 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
LKGKTYLDVPQVTCSPDTSASNITVIYTINNQLRGVELLFNETINVSVKS
GSVLLVVLEEAQRKNPMFKFETTMTSWGLVVSSINNIAENVNHKTYWQFL
SGVTPLNEGVADYIPFNHEHITANFTQY
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 chain2pmv Chain C Residue 1002 [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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PDB2pmv Crystal structure of human intrinsic factor: Cobalamin complex at 2.6-A resolution
Resolution2.6 Å
Binding residue
(original residue number in PDB)		G72 H73 Y115 D153 D204 Y206 S207 Q252 S347 W348 G349 L350 V351 V352 Y367 W368 Q369 F370 P376 L377 N378 E379 G380 Y399
Binding residue
(residue number reindexed from 1)		G66 H67 Y109 D147 D198 Y200 S201 Q246 S326 W327 G328 L329 V330 V331 Y346 W347 Q348 F349 P355 L356 N357 E358 G359 Y378
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:2pmv, PDBe:2pmv, PDBj:2pmv
PDBsum2pmv
PubMed17954916
UniProtP27352|IF_HUMAN Cobalamin binding intrinsic factor (Gene Name=CBLIF)

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