Structure of PDB 6r25 Chain K Binding Site BS04

Receptor Information

>6r25 Chain K (length=737) Species: 9606 (Homo sapiens)

GSRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGEHFCNECFDH
YYRSHKDGYDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKPECR
KWRQLTKEIQLTPQIAKTYRCGMKSDHCSLPEDLRVLEVSNHWWYSMLIL
PPLLKDSVAAPLLSAYYPDCVGMSPSCTGMNRYFQPFYQPNECGKALCVR
PDVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEALTPQKCIPHI
IVRGLVRIRCVQEVERILYFMTRKGLINTGVLSVGADQYLLPKDYHNKSV
IIIGAGPAGLAAARQLHNFGIKVTVLEAKDRIGGRVWDDKSFKGVTVGRG
AQIVNGCINNPVALMCEQLGISMHKFGERCDLIQEGGRITDPTIDKRMDF
HFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKESGIQFSELEGQV
LQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTLLTPGYSVIIEK
LAEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLVTVPLALLQKG
AIQFNPPLSEKKMKAINSLGAGIIEKIALQFPYRFWDSKVQGADFFGHVP
PSASKRGLFAVFYDMDPQKKHSVLMSVIAGEAVASVRTLDDKQVLQQCMA
TLRELFKEQEVPDPTKYFVTRWSTDPWIQMAYSFVKTGGSGEAYDIIAED
IQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAAF

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: 6r25 Chain K Residue 901

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6r25 A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex.
• Resolution: 4.61 Å
• Binding residue (original residue number in PDB): I388 G389 G391 P392 A393 E412 A413 K414 G419 R420 G435 A436 I438 V598 V627 P628 W757 W762 A766 Y767 E795 Q803 T804 V805 A808
• Binding residue (residue number reindexed from 1): I303 G304 G306 P307 A308 E327 A328 K329 G334 R335 G350 A351 I353 V513 V542 P543 W672 W677 A681 Y682 E710 Q718 T719 V720 A723
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): N440
• Catalytic site (residue number reindexed from 1): N355
• 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:6r25, PDBe:6r25, PDBj:6r25
• PDBsum: 6r25
• PubMed: 30970244
• UniProt: Q8NB78|KDM1B_HUMAN Lysine-specific histone demethylase 2 (Gene Name=KDM1B)