Structure of PDB 7xe2 Chain B Binding Site BS06

Receptor Information

>7xe2 Chain B (length=741) Species: 9606 (Homo sapiens)

KYRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGEHFCNECFDH
YYRSHKDGYDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKPECR
KWRQLTKEIQLTPQIAKTYRCGMKSDHCSLPEDLRVLEVSNHWWYSMLIL
PPLLKDSVAAPLLSAYYPDCVGMSPSCTSTNRGMNRYFQPFYQPNECGKA
LCVRPDVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEALTPQKC
IPHIIVRGLVRIRCVQEVERILYFMTRKGLINTGVLSVGADQYLLPKDYH
NKSVIIIGAGPAGLAAARQLHNFGIKVTVLEAKDRIGGRVWDDKSFKGVT
VGRGAQIVNGCINNPVALMCEQLGISMHKFGERCDLIQEGGRITDPTIDK
RMDFHFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKESGIQFSEL
EGQVLQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTLLTPGYSV
IIEKLAEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLVTVPLAL
LQKGAIQFNPPLSEKKMKAINSLGAGIIEKIALQFPYRFWDSKVQGADFF
GHVPPSASKRGLFAVFYDMDPQKKHSVLMSVIAGEAVASVRTLDDKQVLQ
QCMATLRELFKEQEVPDPTKYFVTRWSTDPWIQMAYSFVKTGGSGEAYDI
IAEDIQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAAF

Ligand information

• Ligand ID: FAD
• InChI: InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
• InChIKey: VWWQXMAJTJZDQX-UYBVJOGSSA-N
• SMILES:
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
  ACDLabs 10.04: O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
• Formula: C27 H33 N9 O15 P2
• Name: FLAVIN-ADENINE DINUCLEOTIDE
• ChEMBL: CHEMBL1232653
• DrugBank: DB03147
• ZINC: ZINC000008215434
• PDB chain: 7xe2 Chain B Residue 906

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7xe2 Structure-Activity Relationship and In Silico Evaluation of cis- and trans-PCPA-Derived Inhibitors of LSD1 and LSD2
• Resolution: 2.05 Å
• Binding residue (original residue number in PDB): I388 G389 G391 P392 A393 E412 A413 K414 G419 R420 G435 A436 Q437 I438 P597 V598 V627 P628 I637 I659 W757 W762 I763 A766 Y767 G794 E795 Q803 T804 V805 A808
• Binding residue (residue number reindexed from 1): I307 G308 G310 P311 A312 E331 A332 K333 G338 R339 G354 A355 Q356 I357 P516 V517 V546 P547 I556 I578 W676 W681 I682 A685 Y686 G713 E714 Q722 T723 V724 A727
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 1.14.99.66: [histone-H3]-N(6),N(6)-dimethyl-L-lysine(4) FAD-dependent demethylase.

Gene Ontology

Molecular Function

• GO:0003682 chromatin binding
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0016491 oxidoreductase activity
• GO:0032452 histone demethylase activity
• GO:0032453 histone H3K4 demethylase activity
• GO:0042393 histone binding
• GO:0046872 metal ion binding
• GO:0050660 flavin adenine dinucleotide binding
• GO:0071949 FAD binding
• GO:0140682 FAD-dependent H3K4me/H3K4me3 demethylase activity

Biological Process

• GO:0006325 chromatin organization
• GO:0006338 chromatin remodeling
• GO:0044726 epigenetic programing of female pronucleus
• GO:0071514 genomic imprinting

Cellular Component

• GO:0000786 nucleosome
• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005694 chromosome

External links

• PDB: RCSB:7xe2, PDBe:7xe2, PDBj:7xe2
• PDBsum: 7xe2
• UniProt: Q8NB78|KDM1B_HUMAN Lysine-specific histone demethylase 2 (Gene Name=KDM1B)