Structure of PDB 7qbd Chain A Binding Site BS01

Receptor Information

>7qbd Chain A (length=400) Species: 9606 (Homo sapiens)

EMCEIPEMDSHLVEKLGQHLLPWMDRLSLEHLNPSIYVGLRLSSLQAGTK
EDLYLHSLKLGYQQCLLGCQGKPSMGQLALYLLALRANCEFVRGHKGDRL
VSQLKWFLEDEKRAIGHDHKGHPHTSYYQYGLGILALCLHQKRVHDSVVD
KLLYAVEPFHQGHHSVDTAAMAGLAFTCLKRSNFNPGRRQRITMAIRTVQ
EEILKAQTPEGHFGNVYSTPLALQFLMTSPMRGAELGTACLKARVALLAS
LQDGAFQNALMISQLLPVLNHKTYIDLIFPDCLAPRVMLEPAAETIPQTQ
EIISVTLQVLSLLPPYRQSISVLAGSTVEDVLKKAHELGGFTYETQASLS
GPYLTSVMGKAAGEREFWQLLRDPNTPLLQGIADYRPKDGETIELRLVSW

Ligand information

• Ligand ID: CNC
• InChI: InChI=1S/C62H90N13O14P.CN.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;1-2;/h20-21,23,28,31,34-37,41,52-53,56-57,76,84H,12-19,22,24-27H2,1-11H3,(H15,63,64,65,66,67,68,69,71,72,73,74,77,78,79,80,81,82,83,85,86);;/q;;+3/p-1/t31-,34-,35-,36-,37+,41-,52-,53-,56?,57+,59-,60+,61+,62+;;/m1../s1
• InChIKey: SYZBZQWSWIJYAR-UVKKECPRSA-M
• SMILES:
  CACTVS 3.385: C[CH](CNC(=O)CC[C]1(C)[CH](CC(N)=O)[CH]2[N]([Co++]C#N)C1=C(C)C3=NC(=CC4=NC(=C(C)C5=N[C]2(C)[C](C)(CC(N)=O)[CH]5CCC(N)=O)[C](C)(CC(N)=O)[CH]4CCC(N)=O)C(C)(C)[CH]3CCC(N)=O)O[P](O)(=O)O[CH]6[CH](O)[CH](O[CH]6CO)n7cnc8cc(C)c(C)cc78
  CACTVS 3.385: C[C@H](CNC(=O)CC[C@]1(C)[C@@H](CC(N)=O)[C@H]2[N@@]([Co++]C#N)C1=C(C)C3=NC(=CC4=NC(=C(C)C5=N[C@]2(C)[C@@](C)(CC(N)=O)[C@@H]5CCC(N)=O)[C@@](C)(CC(N)=O)[C@@H]4CCC(N)=O)C(C)(C)[C@@H]3CCC(N)=O)O[P](O)(=O)O[C@H]6[C@@H](O)[C@H](O[C@@H]6CO)n7cnc8cc(C)c(C)cc78
  ACDLabs 12.01: NC(=O)CC1(C)C2=C(C)C=3C(CCC(N)=O)C(C)(CC(N)=O)C4(C)N=3[Co+2]35(C#N)N2=C(C=C2n3c(C(CCC(N)=O)C2(C)C)c(C)c2n5C4C(CC(N)=O)C2(C)CCC(=O)NCC(C)OP(=O)(O)OC2C(CO)OC(n3cnc4cc(C)c(C)cc43)C2O)C1CCC(N)=O
  OpenEye OEToolkits 2.0.7: Cc1cc2c(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(N5C4=C(C1=[N]8C(=CC2=[N]9C(=C7C)C(C2CCC(=O)N)(C)CC(=O)N)C(C1CCC(=O)N)(C)C)C)C#N)CCC(=O)N)(C)CC(=O)N)C)CC(=O)N)C)O
  OpenEye OEToolkits 2.0.7: Cc1cc2c(cc1C)n(cn2)[C@@H]3[C@@H]([C@@H]([C@H](O3)CO)O[P@@](=O)(O)O[C@H](C)CNC(=O)CC[C@@]4([C@H](C5[C@]6([C@@]([C@@H](C7=[N]6[Co+2]89(N5C4=C(C1=[N]8C(=CC2=[N]9C(=C7C)[C@@]([C@@H]2CCC(=O)N)(C)CC(=O)N)C([C@@H]1CCC(=O)N)(C)C)C)C#N)CCC(=O)N)(C)CC(=O)N)C)CC(=O)N)C)O
• Formula: C63 H89 Co N14 O14 P
• Name: CYANOCOBALAMIN
• PDB chain: 7qbd Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7qbd Generation of nanobodies targeting the human, transcobalamin-mediated vitamin B 12 uptake route.
• Resolution: 4.18 Å
• Binding residue (original residue number in PDB): G85 Q86 Y137 Q138 D176 N224 Y226 M270 S357 L358 S359 G360 P361 Y362 L363 F376 W377 Q378 L379 L387 L388 G390 W409
• Binding residue (residue number reindexed from 1): G76 Q77 Y128 Q129 D167 N215 Y217 M261 S348 L349 S350 G351 P352 Y353 L354 F367 W368 Q369 L370 L378 L379 G381 W400
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0031419 cobalamin binding
• GO:0046872 metal ion 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:0005886 plasma membrane
• GO:0009897 external side of plasma membrane
• GO:0043202 lysosomal lumen

External links

• PDB: RCSB:7qbd, PDBe:7qbd, PDBj:7qbd
• PDBsum: 7qbd
• PubMed: 35218573
• UniProt: P20062|TCO2_HUMAN Transcobalamin-2 (Gene Name=TCN2)