satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of SUMO1-ML786519 adduct bound to SAE (PDB entry 6XOG)
Macromolecule: SUMO-activating enzyme subunit 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 346 residues
Sequence: MVEKEEAGGGISEEEAAQYDRQIRLWGLEAQKRLRASRVLLVGLKGLGAEIAKNLILAGVKGLTMLDHEQVTPEDPGAQFLIRTGSVGRNRAEASLERAQNLNPMVDVKVDTEDIEKKPESFFTQFDAVCLTCCSRDVIVKVDQICHKNSIKFFTGDVFGYHGYTFANLGEHEFVEEKTKVAKVSQGVEDGPDTKRAKLDSSETTMVKKKVVFCPVKEALEVDWSSEKAKAALKRTTSDYFLLQVLLKFRTDKGRDPSSDTYEEDSELLLQIRNDVLDSLGISPDLLPEDFVRYCFSEMAPVCAVVGGILAQEIVKALSQRDPPHNNFFFFDGMKGNGIVECLGPK
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.2064
R free: 0.24
Average B factor: 45.146
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 50 mM BisTris, pH 6.5, 50 mM Ammonium Sulfate, 30% pentaerythritol ethoxylate (Hampton Index 57)
Matthews coefficient: 2.19
Solvent content (%): 43.74
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2021-03-10
JAK2 JH1 in complex with JNJ-7706621 (Crystal Form 2) (PDB entry 6DRW)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 316 residues
Sequence: SYYHHHHHHDYDIPTTENLYFQGDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.303
R work: 0.2143
R free: 0.2552
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 295
Crystal growth procedure: 0.1M Glycyl-glycine pH 8.0
2.5 M Sodium Malonate pH 6.0
Matthews coefficient: 2.46
Solvent content (%): 50.01
Ligand: 4-({5-amino-1-[(2,6-difluorophenyl)carbonyl]-1H-1,2,4-triazol-3-yl}amino)benzenesulfonamide (SKE)
Ligand formula: C15 H12 F2 N6 O3 S
Ligand molecular weight: 394.356
Ligand SMILES: c1cc(c(c(c1)F)C(=O)n2c(nc(n2)Nc3ccc(cc3)S(=O)(=O)N)N)F
Ligand InChI: InChI=1S/C15H12F2N6O3S/c16-10-2-1-3-11(17)12(10)13(24)23-14(18)21-15(22-23)20-8-4-6-9(7-5-8)27(19,25)26/h1-7H,(H2,19,25,26)(H3,18,20,21,22)
Release date: 2018-07-18
Crystal structure of the G308E mutant of human apoptosis inducing factor (PDB entry 5FS8)
Macromolecule: APOPTOSIS-INDUCING FACTOR 1, MITOCHONDRIAL
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1
Sequence length: 515 residues
Sequence: GLTPEQKQKKAALSASEGEEVPQDKAPSHVPFLLIGGGTAAFAAARSIRARDPGARVLIVSEDPELPYMRPPLSKELWFSDDPNVTKTLRFKQWNGKERSIYFQPPSFYVSAQDLPHIENGGVAVLTGKKVVQLDVRDNMVKLNDGSQITYEKCLIATGGTPRSLSAIDRAGAEVKSRTTLFRKIGDFRSLEKISREVKSITIIGEGFLGSELACALGRKARALGTEVIQLFPEKGNMGKILPEYLSNWTMEKVRREGVKVMPNAIVQSVGVSSGKLLIKLKDGRKVETDHIVAAVGLEPNVELAKTGGLEIDSDFGGFRVNAELQARSNIWVAGDAACFYDIKLGRRRVEHHDHAVVSGRLAGENMTGAAKPYWHQSMFWSDLGPDVGYEAIGLVDSSLPTVGVFAKATAQDNPKSATEQSGTGIRSESETESRASEITIPPSTPAVPQAPVQGEDYGKGVIFYLRDKVVVGIVLWNIFNRMPIARKIIKDGEQHEDLNEVAKLFNIHEDLVPR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.16443
R free: 0.19247
Average B factor: 23.382
Crystallization pH: 7.5
Crystal growth procedure: 0.2 M AMMONIUM ACETATE AND 20% POLY-ETHYLENE GLYCOL, pH 7.5
Matthews coefficient: 2.45
Solvent content (%): 49.75
Ligand: FLAVIN-ADENINE DINUCLEOTIDE (FAD)
Ligand formula: C27 H33 N9 O15 P2
Ligand molecular weight: 785.55
Ligand SMILES: 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
Ligand 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
Release date: 2016-05-11
Small Molecule inhibitors of IAP (PDB entry 5M6F)
Macromolecule: E3 ubiquitin-protein ligase XIAP
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 127 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMNFPNSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTHSLEECLVR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.39
R work: 0.202
R free: 0.261
Average B factor: 45.004
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M HEPES/NaOHpH=8, 3.3M NaCl,
Matthews coefficient: 4.67
Solvent content (%): 73.68
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2017-05-24
The crystal structure of the complex of hCAVII with 2-(4-benzhydrylpiperazin-1-yl)-N-(4-sulfamoylphenyl)acetamide (PDB entry 6ZR9)
Macromolecule: Carbonic anhydrase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 274 residues
Sequence: MGMTGHHGWGYGQDDGPSHWHKLYPIAQGDRQSPINIISSQAVYSPSLQPLELSYEACMSLSITNNGHSVQVDFNDSDDRTVVTGGPLEGPYRLKQFHFHWGKKHDVGSEHTVDGKSFPSELHLVHWNAKKYSTFGEAASAPDGLAVVGVFLETGDEHPSMNRLTDALYMVRFKGTKAQFSCFNPKSLLPASRHYWTYPGSLTTPPLSESVTWIVLREPISISERQMGKFRSLLFTSEDDERIHMVNNFRPPQPLKGRVVKASFRALEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.196
R free: 0.2411
Average B factor: 25.2641
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG 3350, 0.2 M Ammonium acetate, 0.1 M Tris-HCl (pH 8.5)
Matthews coefficient: 2.12
Solvent content (%): 41.96
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2021-06-16
X-ray structure of PI3Kinase Gamma in complex with Copanlisib (PDB entry 5G2N)
Macromolecule: PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT GAMMA ISOFORM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.137
Sequence length: 980 residues
Sequence: MLLGSSEESQAFQRQLTALIGYDVTDVSNVHDDELEFTRRGLVTPRMAEVASRDPKLYAMHPWVTSKPLPEYLWKKIANNCIFIVIHRSTTSQTIKVSPDDTPGAILQSFFTKMAKKKSLMDIPESQSEQDFVLRVCGRDEYLVGETPIKNFQWVRHCLKNGEEIHVVLDTPPDPALDEVRKEEWPLVDDCTGVTGYHEQLTIHGKDHESVFTVSLWDCDRKFRVKIRGIDIPVLPRNTDLTVFVEANIQHGQQVLCQRRTSPKPFTEEVLWNVWLEFSIKIKDLPKGALLNLQIYCGKAPALSSKASAESPSSESKGKVQLLYYVNLLLIDHRFLLRRGEYVLHMWQISGKGEDQGSFNADKLTSATNPDKENSMSISILLDNYCHPIALPKHQPTPDPEGDRVRAEMPNQLRKQLEAIIATDPLNPLTAEDKELLWHFRYESLKHPKAYPKLFSSVKWGQQEIVAKTYQLLARREVWDQSALDVGLTMQLLDCNFSDENVRAIAVQKLESLEDDDVLHYLLQLVQAVKFEPYHDSALARFLLKRGLRNKRIGHFLFWFLRSEIAQSRHYQQRFAVILEAYLRGCGTAMLHDFTQQVQVIEMLQKVTLDIKSLSAEKYDVSSQVISQLKQKLENLQNSQLPESFRVPYDPGLKAGALAIEKCKVMASKKKPLWLEFKCADPTALSNETIGIIFKHGDDLRQDMLILQILRIMESIWETESLDLCLLPYGCISTGDKIGMIEIVKDATTIAKIQQSTVGNTGAFKDEVLNHWLKEKSPTEEKFQAAVERFVYSCAGYCVATFVLGIGDRHNDNIMITETGNLFHIDFGHILGNYKSFLGINKERVPFVLTPDFLFVMGTSGKKTSPHFQKFQDICVKAYLALRHHTNLLIILFSMMLMTGMPQLTSKEDIEYIRDALTVGKNEEDAKKYFLDQIEVCRDKGWTVQFNWFLHLVLGIKQGEKHSAEFGLVPRGSGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.68
R work: 0.21142
R free: 0.28454
Average B factor: 70.627
Crystal growth procedure: 19% PEG4000,0.15M (NH4)2SO4, 0.1M TRIS PH7.5
Matthews coefficient: 2.46
Solvent content (%): 50.01
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2016-04-20
Crystal structure of the Tudor domain of human ERCC6-L2 (PDB entry 6HQ9)
Macromolecule: DNA excision repair protein ERCC-6-like 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4
Sequence length: 69 residues
Sequence: SMKDIWHPGERCLAPSPDNGKLCEASIKSITVDENGKSFAVVLYADFQERKIPLKQLQEVKFVKDCPRN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.982
R work: 0.2243
R free: 0.2473
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M Ammonium sulphate, 0.1 M Acetate pH 4.5, 18% PEG 4000
Matthews coefficient: 2.22
Solvent content (%): 44.7
Release date: 2018-10-17
Crystal structure of human carbonic anhydrase isozyme XIII with 2,3,5,6-Tetrafluoro-4-(propylthio)benzenesulfonamide (PDB entry 5LLN)
Macromolecule: Carbonic anhydrase 13
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 263 residues
Sequence: MMSRLSWGYREHNGPIHWKEFFPIADGDQQSPIEIKTKEVKYDSSLRPLSIKYDPSSAKIISNSGHSFNVDFDDTENKSVLRGGPLTGSYRLRQVHLHWGSADDHGSEHIVDGVSYAAELHVVHWNSDKYPSFVEAAHEPDGLAVLGVFLQIGEPNSQLQKITDTLDSIKEKGKQTRFTNFDLLSLLPPSWDYWTYPGSLTVPPLLESVTWIVLKQPINISSQQLAKFRSLLCTAEGEAAAFLVSNHRPPQPLKGRKVRASFH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1682
R free: 0.2057
Average B factor: 16.125
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer: 0.1M ammonium citrate (pH 5) and 20% PEG4000
Matthews coefficient: 2.18
Solvent content (%): 43.7
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2017-08-16
Crystal structure for the complex of human carbonic anhydrase IV and ethoxyzolamide (PDB entry 5JN9)
Macromolecule: Carbonic anhydrase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 266 residues
Sequence: AESHWCYEVQAESSNYPCLVPVKWGGNCQKDRQSPINIVTTKAKVDKKLGRFFFSGYDKKQTWTVQNNGHSVMMLLENKASISGGGLPAPYQAKQLHLHWSDLPYKGSEHSLDGEHFAMEMHIVHEKEKGTSRNVKEAQDPEDEIAVLAFLVEAGTQVNEGFQPLVEALSNIPKPEMSTTMAESSLLDLLPKEEKLRHYFRYLGSLTTPTCDEKVVWTVFREPIQLHREQILAFSQKLYYDKEQTVSMKDNVRPLQQLGQRTVIKS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.17
R free: 0.22
Average B factor: 29.55
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM Na acetate, 200 mM AmSO4 and 16% PEG 3350
Matthews coefficient: 2.5
Solvent content (%): 51.3
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2017-05-03
CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX; WITH AN INHIBITOR 5-((R)-1-[1,2,4]Triazolo[1,5-a]pyrimidin-7-yl-pyrrolidin-2-ylmethoxy)-isoquinoline (PDB entry 5LYX)
Macromolecule: Methionine aminopeptidase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.11.18
Sequence length: 378 residues
Sequence: MGPKVQTDPPSVPICDLYPNGVFPKGQECEYPPTQDGRTAAWRTTSEEKKALDQASEEIWNDFREAAEAHRQVRKYVMSWIKPGMTMIEICEKLEDCSRKLIKENGLNAGLAFPTGCSLNNCAAHYTPNAGDTTVLQYDDICKIDFGTHISGRIIDCAFTVTFNPKYDTLLKAVKDATNTGIKCAGIDVRLCDVGEAIQEVMESYEVEIDGKTYQVKPIRNLNGHSIGQYRIHAGKTVPIVKGGEATRMEEGEVYAIETFGSTGKGVVHDDMECSHYMKNFDVGHVPIRLPRTKHLLNVINENFGTLAFCRRWLDRLGESKYLMALKNLCDLGIVDPYPPLCDIKGSYTAQFEHTILLRPTCKEVVSRGDDYHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.195
R free: 0.217
Average B factor: 48.86
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 20% methanol, 0.1 M citrate
Matthews coefficient: 2.65
Solvent content (%): 53.56
Ligand: 5-[[(2~{R})-1-([1,2,4]triazolo[1,5-a]pyrimidin-7-yl)pyrrolidin-2-yl]methoxy]isoquinoline (7BF)
Ligand formula: C19 H18 N6 O
Ligand molecular weight: 346.386
Ligand SMILES: c1cc2cnccc2c(c1)OCC3CCCN3c4ccnc5n4ncn5
Ligand InChI: InChI=1S/C19H18N6O/c1-3-14-11-20-8-6-16(14)17(5-1)26-12-15-4-2-10-24(15)18-7-9-21-19-22-13-23-25(18)19/h1,3,5-9,11,13,15H,2,4,10,12H2/t15-/m1/s1
Release date: 2017-08-16
STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM I MYRISTOLEATE COMPLEX - 2.1A (PDB entry 4UZL)
Macromolecule: PROTEIN NOTUM HOMOLOG
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.1
Sequence length: 386 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSAAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTHHHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.21358
R free: 0.25332
Average B factor: 65.249
Crystallization pH: 5
Crystal growth procedure: 10 %W/V POLYETHYLENE GLYCOL 6000, 0.1 M CITRATE PH 5.0
Matthews coefficient: 2.2
Solvent content (%): 45
Ligand: Myristoleic acid (MYZ)
Ligand formula: C14 H26 O2
Ligand molecular weight: 226.355
Ligand SMILES: CCCCC=CCCCCCCCC(=O)O
Ligand InChI: InChI=1S/C14H26O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14(15)16/h5-6H,2-4,7-13H2,1H3,(H,15,16)/b6-5-
Release date: 2015-02-25
High-resolution isotropic multiconformer synchrotron model of CypA at 273 K (PDB entry 5F66)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 165 residues
Sequence: MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.15
R work: 0.1788
R free: 0.195
Average B factor: 21.3652
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT.
Matthews coefficient: 2.81
Solvent content (%): 56.3
Release date: 2015-12-30
Crystal structure of human phosphodiesterase 4B catalytic domain with inhibitor NPD-001 (PDB entry 5LAQ)
Macromolecule: cAMP-specific 3',5'-cyclic phosphodiesterase 4B,cAMP-specific 3',5'-cyclic phosphodiesterase 4B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.53
Sequence length: 421 residues
Sequence: MSVSEMASNKFKRMLNRELTHLSEMSRSGNQVSEYISNTFLDKQNDVEIPKVTAEEAPQPMTQISGVKKLMHSSSLNNTSISRFGVNTENEDHLAKELEDLNKWGLNIFNVAGYSHNRPLTCIMYAIFQERDLLKTFRISSDTFITYMMTLEDHYHSDVAYHNSLHAADVAQSTHVLLSTPALDAVFTDLEILAAIFAAAIHDVDHPGVSNQFLINTNSELALMYNDESVLENHHLAVGFKLLQEEHCDIFMNLTKKQRQTLRKMVIDMVLATDMSKHMSLLADLKTMVETKKVTSSGVLLLDNYTDRIQVLRNMVHCADLSNPTKSLELYRQWTDRIMEEFFQQGDKERERGMEISPMCDKHTASVEKSQVGFIDYIVHPLWETWADLVQPDAQDILDTLEDNRNWYQSMIPQSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.17113
R free: 0.24084
Average B factor: 51.062
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 293
Crystal growth procedure: 50 mM calcium acetate, 20% PEG 400, 100 mM sodium acetate
Matthews coefficient: 2.35
Solvent content (%): 47.6
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2018-03-14
Crystal structure of human phosphodiesterase 2A with N-(1-adamantyl)-1-(2-chlorophenyl)-4-methyl-[1,2,4]triazolo[4,3-a]quinoxaline-8-carboxamide (PDB entry 6C7D)
Macromolecule: cGMP-dependent 3',5'-cyclic phosphodiesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 342 residues
Sequence: SAMDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.79
R work: 0.1868
R free: 0.2319
Average B factor: 32.1304
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.4
Crystallization temperature (K): 293
Crystal growth procedure: 17-19% PEG3350, 0.2 M magnesium chloride, 0.1 M Tris, pH 8.4
Matthews coefficient: 2.21
Solvent content (%): 44.47
Ligand: 1-(2-chlorophenyl)-4-methyl-N-[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]decan-1-yl][1,2,4]triazolo[4,3-a]quinoxaline-8-carboxamide (EOJ)
Ligand formula: C27 H26 Cl N5 O
Ligand molecular weight: 471.981
Ligand SMILES: Cc1c2nnc(n2c3cc(ccc3n1)C(=O)NC45CC6CC(C4)CC(C6)C5)c7ccccc7Cl
Ligand InChI: InChI=1S/C27H26ClN5O/c1-15-24-31-32-25(20-4-2-3-5-21(20)28)33(24)23-11-19(6-7-22(23)29-15)26(34)30-27-12-16-8-17(13-27)10-18(9-16)14-27/h2-7,11,16-18H,8-10,12-14H2,1H3,(H,30,34)/t16-,17+,18-,27-
Release date: 2018-08-15
Crystal Structure Of Aldose Reductase (AKR1B1) Complexed With NADP+ And AT-003 Soaked In Hydrogen Peroxide (PDB entry 8FH8)
Macromolecule: Aldo-keto reductase family 1 member B1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.300
Sequence length: 316 residues
Sequence: MASRLLLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQEKLREQVVKREELFIVSKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGKEFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGISNFNHLQVEMILNKPGLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAKHNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCALLSCTSHKDYPFHEEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1666
R free: 0.1948
Average B factor: 18.543
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 298
Crystal growth procedure: 25% PEG 3,350, 100 mM Bis-Tris
Matthews coefficient: 2.24
Solvent content (%): 45.17
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2023-12-20
Discovery of a novel class of highly potent inhibitors of the p53-MDM2 interaction by structure-based design starting from a conformational argument (PDB entry 5LN2)
Macromolecule: E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 96 residues
Sequence: GSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.58
R work: 0.2148
R free: 0.2474
Average B factor: 19.35
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 298
Crystal growth procedure: 2.5M (NH4)2SO4, 0.1M NaCitrate
Matthews coefficient: 2.15
Solvent content (%): 42.78
Ligand: (4~{S})-5-[5-chloranyl-2-[2-(dimethylamino)ethoxy]phenyl]-4-(4-chloranyl-2-methyl-phenyl)-2-(2-methoxyphenyl)-3-propan-2-yl-4~{H}-pyrrolo[3,4-c]pyrazol-6-one (6ZT)
Ligand formula: C32 H34 Cl2 N4 O3
Ligand molecular weight: 593.543
Ligand SMILES: Cc1cc(ccc1C2c3c(nn(c3C(C)C)c4ccccc4OC)C(=O)N2c5cc(ccc5OCCN(C)C)Cl)Cl
Ligand InChI: InChI=1S/C32H34Cl2N4O3/c1-19(2)30-28-29(35-38(30)24-9-7-8-10-26(24)40-6)32(39)37(31(28)23-13-11-21(33)17-20(23)3)25-18-22(34)12-14-27(25)41-16-15-36(4)5/h7-14,17-19,31H,15-16H2,1-6H3/t31-/m0/s1
Release date: 2016-09-07
Integrin beta5(743-774)-linker-PAK4cat(D440N/S474E) (PDB entry 7S47)
Macromolecule: Integrin beta-5, Isoform 2 of Serine/threonine-protein kinase PAK 4 chimera
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 383 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMKLLVTIHDRREFAKFQSERSRARYEMASNPLYSSGSSGSSGSSGARARQENGMPEKPPGPRSPQREPQRVSHEQFRAALQLVVDPGDPRSYLDNFIKIGEGSTGIVCIATVRSSGKLVAVKKMDLRKQQRRELLFNEVVIMRDYQHENVVEMYNSYLVGDELWVVMEFLEGGALTDIVTHTRMNEEQIAAVCLAVLQALSVLHAQGVIHRNIKSDSILLTHDGRVKLSDFGFCAQVSKEVPRRKELVGTPYWMAPELISRLPYGPEVDIWSLGIMVIEMVDGEPPYFNEPPLKAMKMIRDNLPPRLKNLHKVSPSLKGFLDRLLVRDPAQRATAAELLKHPFLAKAGPPASIVPLMRQNRTR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1935
R free: 0.2369
Average B factor: 36.138
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM sodium acetate pH 4.0, 0.7 M diammonium phosphate
Matthews coefficient: 1.85
Solvent content (%): 33.36
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP)
Ligand formula: C10 H17 N6 O12 P3
Ligand molecular weight: 506.196
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
Release date: 2022-11-09
Zinc-Free APOBEC3F Catalytic Domain Crystal Structure (PDB entry 5HX4)
Macromolecule: DNA dC->dU-editing enzyme APOBEC-3F
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.4
Sequence length: 199 residues
Sequence: GPLGSPGIPGKEILRNPMEAMDPHIFYFHFKNLRKAYGRNESWLCFTMEVVKHHSPVSWKRGVFRNQVDPETGRHAERCFLSWFADDILSPNTNYEVTWYTSWSPCPECAGEVAEFLARHSNVNLTIKTARLYYFDDTDYQEGLRSLSQEGASVEIMGYKDFKYCWENFVYNDDEPFKPWDGLDYNFLDLDSKLQEILE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.92
R work: 0.1848
R free: 0.2137
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: Tacsimate pH5.0, PEG3350, Glycerol
Matthews coefficient: 1.98
Solvent content (%): 37.82
Release date: 2016-05-18
Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G5-006 (PDB entry 7ZMT)
Macromolecule: ATP-dependent DNA helicase Q5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.12
Sequence length: 445 residues
Sequence: SMDPERRVRSTLKKVFGFDSFKTPLQESATMAVVKGNKDVFVCMPTGAGKSLCYQLPALLAKGITIVVSPLIALIQDQVDHLLTLKVRVSSLNSKLSAQERKELLADLEREKPQTKILYITPEMAASSSFQPTLNSLVSRHLLSYLVVDEAHCVSQWGHDFRPDYLRLGALRSRLGHAPCVALTATATPQVQEDVFAALHLKKPVAIFKTPCFRANLFYDVQFKELISDPYGNLKDFCLKALGQEADKGLSGCGIVYCRTREACEQLAIELSCRGVNAKAYHAGLKASERTLVQNDWMEEKVPVIVATISFGMGVDKANVRFVAHWNIAKSMAGYYQESGRAGRDGKPSWCRLYYSRNDRDQVSFLIRKEVAKLQEKRGNKASDKATIMAFDALVTFCEELGCRHAAIAKYFGDALPACAKGCDHCQNPTAVRRRLEALERSSSW
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2636
R free: 0.291
Average B factor: 72.529
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M sodium formate -- 20% PEG3350
Matthews coefficient: 3.25
Solvent content (%): 62.1
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2022-06-22