Structure of PDB 4guu Chain A Binding Site BS02

Receptor Information
>4guu Chain A (length=740) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLGSRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGEHFCNECF
DHYYRSHKDGYDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKPE
CRKWRQLTKEIQLTPQIAKTYRCGMKPNSDHCSLPEDLRVLEVSNHWWYS
MLILPPLLKDSVAAPLLSAYYPDCVGMSPSCTGMNRYFQPFYQPNECGKA
LCVRPDVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEALTPQKC
IPHIIVRGLVRIRCVQEVERILYFMTRKGLINTGVLSVGADQYLLPKDYH
NKSVIIIGAGPAGLAAARQLHNFGIKVTVLEAKDRIGGRVWDDKSFKGVT
VGRGAQIVNGCINNPVALMCEQLGISMHKFGERCDLIQEGGRITDPTIDK
RMDFHFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKESGIQFSEL
EGQVLQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTLLTPGYSV
IIEKLAEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLVTVPLAL
LQKGAIQFNPPLSEKKMKAINSLGAGIIEKIALQFPYRFWDSKVQGADFF
GHVPPSASKRGLFAVFYDMDPQKKHSVLMSVIAGEAVASVRTLDDKQVLQ
QCMATLRELFKEQEVPDPTKYFVTRWSTDPWIQMAYSFVKTGGSGEAYDI
IAEDIQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAA
Ligand information
Ligand IDFA9
InChIInChI=1S/C36H43N9O16P2/c1-16-8-20-21(9-17(16)2)45-25(48)10-19(18-6-4-3-5-7-18)36(45)33(41-35(53)42-34(36)52)43(20)11-22(46)27(49)23(47)12-58-62(54,55)61-63(56,57)59-13-24-28(50)29(51)32(60-24)44-15-40-26-30(37)38-14-39-31(26)44/h3-9,14-15,19,22-24,27-29,32-33,46-47,49-51H,10-13H2,1-2H3,(H,54,55)(H,56,57)(H2,37,38,39)(H2,41,42,52,53)/t19-,22+,23-,24-,27+,28-,29-,32-,33-,36+/m1/s1
InChIKeyQWOOVYWBGZGGNV-ITRBMUPBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N3C(=O)CC(C34C(N2CC(C(C(COP(=O)(O)OP(=O)(O)OCC5C(C(C(O5)n6cnc7c6ncnc7N)O)O)O)O)O)NC(=O)NC4=O)c8ccccc8
CACTVS 3.370Cc1cc2N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH]6NC(=O)NC(=O)[C]67[CH](CC(=O)N7c2cc1C)c8ccccc8
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N3C(=O)CC([C@@]34[C@@H](N2C[C@@H]([C@@H]([C@@H](COP(=O)(O)OP(=O)(O)OC[C@@H]5[C@H]([C@H]([C@@H](O5)n6cnc7c6ncnc7N)O)O)O)O)O)NC(=O)NC4=O)c8ccccc8
CACTVS 3.370Cc1cc2N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@H]6NC(=O)NC(=O)[C@]67[C@H](CC(=O)N7c2cc1C)c8ccccc8
ACDLabs 12.01O=C4N2c1cc(c(cc1N(C5NC(=O)NC(=O)C25C(c3ccccc3)C4)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC8OC(n7cnc6c(ncnc67)N)C(O)C8O)C)C
FormulaC36 H43 N9 O16 P2
Name[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(3R,3aS,7aR)-10,11-dimethyl-1,4,6-trioxo-3-phenyl-2,3,5,6,7,7a-hexahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate
ChEMBL
DrugBank
ZINCZINC000263620959
PDB chain4guu Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4guu LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation
Resolution2.302 Å
Binding residue
(original residue number in PDB)
I388 G389 P392 A393 E412 A413 K414 G419 R420 G435 A436 Q437 I438 Y545 V598 V627 P628 I659 W757 W762 A766 Y767 G794 E795 Q803 T804 V805 A808
Binding residue
(residue number reindexed from 1)
I307 G308 P311 A312 E331 A332 K333 G338 R339 G354 A355 Q356 I357 Y464 V517 V546 P547 I578 W676 W681 A685 Y686 G713 E714 Q722 T723 V724 A727
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) N440
Catalytic site (residue number reindexed from 1) N359
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

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:4guu, PDBe:4guu, PDBj:4guu
PDBsum4guu
PubMed23260659
UniProtQ8NB78|KDM1B_HUMAN Lysine-specific histone demethylase 2 (Gene Name=KDM1B)

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