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5FZ0

Crystal structure of the catalytic domain of human JARID1B in complex with 2,5-dichloro-N-(pyridin-3-yl)thiophene-3-carboxamide (N08137b) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening)

Functional Information from PDB Data
site_idAC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN A 1754
ChainResidue
ACYS692
ACYS695
ACYS715
AHIS718

site_idAC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN A 1755
ChainResidue
ACYS706
ACYS708
ACYS723
ACYS725

site_idAC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE DMS A 1756
ChainResidue
ATYR488
AGLU501
ASER507
AASN601
ATRP486

site_idAC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE DMS A 1757
ChainResidue
ATHR97
AARG98
ASER495
APHE496
ACYS497
ADJ61767

site_idAC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MN A 1758
ChainResidue
AHIS499
AGLU501
AHIS587
ADJ61767
AHOH2032
AHOH2037

site_idAC6
Number of Residues12
DetailsBINDING SITE FOR RESIDUE EPE A 1759
ChainResidue
AILE500
ATRP504
ALEU541
ALEU552
ATYR586
AHIS617
ATYR618
ALEU621
AARG623
AHOH2035
AHOH2045
AHOH2092

site_idAC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO A 1760
ChainResidue
APHE83
AGLY426
AASP428
APHE434
ALEU487

site_idAC8
Number of Residues2
DetailsBINDING SITE FOR RESIDUE EDO A 1761
ChainResidue
AARG666
AHOH2093

site_idAC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO A 1762
ChainResidue
AARG612
AASP630
AMET658
AGLU662
AHOH2088

site_idBC1
Number of Residues2
DetailsBINDING SITE FOR RESIDUE EDO A 1763
ChainResidue
AGLY524
AARG584

site_idBC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO A 1764
ChainResidue
AARG670
AVAL674
AILE675
ALEU732
AHOH2068

site_idBC3
Number of Residues8
DetailsBINDING SITE FOR RESIDUE EDO A 1765
ChainResidue
ATYR425
ATYR488
ASER494
ASER495
ALYS517
AASN591
ADJ61767
AHOH2042

site_idBC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE CL A 1766
ChainResidue
ALEU90
AASN91
ALEU413
ATHR416
AGLU419

site_idBC5
Number of Residues16
DetailsBINDING SITE FOR RESIDUE DJ6 A 1767
ChainResidue
AARG86
AARG98
AVAL99
ATYR425
ATYR488
ASER495
APHE496
AHIS499
AHIS587
ADMS1757
AMN1758
AEDO1765
AHOH2032
AHOH2037
AHOH2040
AHOH2042

site_idBC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PO4 A 1768
ChainResidue
AHIS622
ALYS694
AHIS718
AHOH2054

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues52
DetailsZN_FING: C5HC2 => ECO:0000269|PubMed:26741168, ECO:0000269|PubMed:27214403, ECO:0000269|PubMed:28262558
ChainResidueDetails
ACYS692-MET744

site_idSWS_FT_FI2
Number of Residues4
DetailsBINDING: BINDING => ECO:0000250|UniProtKB:P29375
ChainResidueDetails
ATYR425
ASER507
AASN509
ALYS517

site_idSWS_FT_FI3
Number of Residues3
DetailsBINDING: BINDING => ECO:0000305|PubMed:26741168, ECO:0000305|PubMed:27214403, ECO:0000305|PubMed:28262558
ChainResidueDetails
AHIS499
AGLU501
AHIS587

site_idSWS_FT_FI4
Number of Residues2
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:25755297, ECO:0007744|PubMed:28112733
ChainResidueDetails
ALYS769

218853

PDB entries from 2024-04-24

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