satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure of Human NEIL1, Free Protein (PDB entry 5ITQ)
Macromolecule: Endonuclease 8-like 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2
Sequence length: 290 residues
Sequence: MPEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRESVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQHRPSPELTLSQKIRTKLQNPDLLELCHSVPKEVVQLGGRGYGSESGEEDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.48
R work: 0.156
R free: 0.196
Crystallization method: EVAPORATION
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M cacodylic acid (pH 7.0), 0.1M NaCl, 0.05 M MgCl2, 24%(w/v) PEG 8000
Matthews coefficient: 2.62
Solvent content (%): 53.03
Release date: 2016-07-06
Tankyrase 2 in complex with an inhibitor (OM-153) (PDB entry 7O6X)
Macromolecule: Poly [ADP-ribose] polymerase tankyrase-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 171 residues
Sequence: SMLNTSGSGTILIDLSPDDKEFQSVEEEMQSTVREHRDGGHAGGIFNRYNILKIQKVCNKKLWERYTHRRKEVSEENHNHANERMLFHGSPFVNAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPVHKDRSCYICHRQLLFCRVTLGKSFLQFSAMK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2112
R free: 0.2582
Average B factor: 38.595
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295.15
Crystal growth procedure: 22.5% PEG6000, Bicine pH=8.75
Matthews coefficient: 2.35
Solvent content (%): 47.72
Ligand: N-[3-[5-(5-ethoxypyridin-2-yl)-4-(2-fluorophenyl)-1,2,4-triazol-3-yl]cyclobutyl]quinoxaline-5-carboxamide (V4Q)
Ligand formula: C28 H24 F N7 O2
Ligand molecular weight: 509.534
Ligand SMILES: CCOc1ccc(nc1)c2nnc(n2c3ccccc3F)C4CC(C4)NC(=O)c5cccc6c5nccn6
Ligand InChI: InChI=1S/C28H24FN7O2/c1-2-38-19-10-11-23(32-16-19)27-35-34-26(36(27)24-9-4-3-7-21(24)29)17-14-18(15-17)33-28(37)20-6-5-8-22-25(20)31-13-12-30-22/h3-13,16-18H,2,14-15H2,1H3,(H,33,37)/t17-,18-
Release date: 2022-01-12
Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Olaparib (AZD2281) (PDB entry 8HLJ)
Macromolecule: Poly [ADP-ribose] polymerase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 353 residues
Sequence: GPESQLDLRVQELIKLICNVQAMEEMMMEMKYNTKKAPLGKLTVAQIKAGYQSLKKIEDCIRAGQHGRALMEACNEFYTRIPHDFGLRTPPLIRTQKELSEKIQLLEALGDIEIAIKLVKSERQGLEHPLDQHYRNLHCALRPLDHESYEFKVISQYLQSTHAPTHSDYTMTLLDLFEVEKDGEKEAFREDLHNRMLLWHGSRMSNWVGILSHGLRIAPPEAPITGYMFGKGIYFADMSSKSANYCFASRLKNTGLLLLSEVALGQCNELLEANPKAEGLLQGKHSTKGLGKMAPSSAHFVTLNGSTVPLGPASDTGILNPDGYTLNYNEYIVYNPNQVRMRYLLKVQFNFLQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.24
R work: 0.1999
R free: 0.2467
Average B factor: 42.21
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 296.5
Crystal growth procedure: 25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Matthews coefficient: 2.12
Solvent content (%): 41.85
Ligand: 4-(3-{[4-(cyclopropylcarbonyl)piperazin-1-yl]carbonyl}-4-fluorobenzyl)phthalazin-1(2H)-one (09L)
Ligand formula: C24 H23 F N4 O3
Ligand molecular weight: 434.463
Ligand SMILES: c1ccc2c(c1)C(=NNC2=O)Cc3ccc(c(c3)C(=O)N4CCN(CC4)C(=O)C5CC5)F
Ligand InChI: InChI=1S/C24H23FN4O3/c25-20-8-5-15(14-21-17-3-1-2-4-18(17)22(30)27-26-21)13-19(20)24(32)29-11-9-28(10-12-29)23(31)16-6-7-16/h1-5,8,13,16H,6-7,9-12,14H2,(H,27,30)
Release date: 2024-05-01
MST3 in complex with MRIA11 (PDB entry 7B33)
Macromolecule: Serine/threonine-protein kinase 24
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 306 residues
Sequence: MRAQLWGLALNKRRATLPHPGGSTNLKADPEELFTKLEKIGKGSFGEVFKGIDNRTQKVVAIKIIDLEEAEDEIEDIQQEITVLSQCDSPYVTKYYGSYLKDTKLWIIMEYLGGGSALDLLEPGPLDETQIATILREILKGLDYLHSEKKIHRDIKAANVLLSEHGEVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDSKADIWSLGITAIELARGEPPHSELHPMKVLFLIPKNNPPTLEGNYSKPLKEFVEACLNKEPSFRPTAKELLKHKFILRNAKKTSYLTELIDAHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1808
R free: 0.2084
Average B factor: 38.84
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Protein solution: 10 mg/ml in buffer 25 mM HEPES pH 7.5, 200 mM NaCl, 5% glycerol, 0.5 mM TCEP.
Reservoir: 19% PEG 3350, 0.1M bis-tris pH 6.8.
Matthews coefficient: 2.59
Solvent content (%): 52.5
Ligand: 8-[(5-azanyl-1,3-dioxan-2-yl)methyl]-6-[4-[6-[bis(fluoranyl)methyl]pyridin-2-yl]-2-chloranyl-phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7-one (SQE)
Ligand formula: C25 H23 Cl F2 N6 O3
Ligand molecular weight: 528.938
Ligand SMILES: CNc1ncc2c(n1)N(C(=O)C(=C2)c3ccc(cc3Cl)c4cccc(n4)C(F)F)CC5OCC(CO5)N
Ligand InChI: InChI=1S/C25H23ClF2N6O3/c1-30-25-31-9-14-7-17(24(35)34(23(14)33-25)10-21-36-11-15(29)12-37-21)16-6-5-13(8-18(16)26)19-3-2-4-20(32-19)22(27)28/h2-9,15,21-22H,10-12,29H2,1H3,(H,30,31,33)/t15-,21-
Release date: 2020-12-16
The Fk1 domain of FKBP51 in complex with the new synthetic ligand 2-(3-((R)-1-((S)-1-((S)-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)acetyl)piperidine-2-carboxamido)-3-(3,4-dimethoxyphenyl)propyl)phenoxy)acetic acid (PDB entry 5DIU)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 128 residues
Sequence: GAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNGKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEICHLLCKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.1441
R free: 0.1852
Average B factor: 21.323
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 10 % PEG-3350, 0.2 M NH4-acetate and 0.1 M HEPES-NaOH pH 7.5
Matthews coefficient: 2.21
Solvent content (%): 44.27
Ligand: {3-[(1R)-1-[({(2S)-1-[(2S)-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)acetyl]piperidin-2-yl}carbonyl)amino]-3-(3,4-dimethoxyphenyl)propyl]phenoxy}acetic acid (5BG)
Ligand formula: C42 H54 N2 O10
Ligand molecular weight: 746.886
Ligand SMILES: COc1ccc(cc1OC)CCC(c2cccc(c2)OCC(=O)O)NC(=O)C3CCCCN3C(=O)C(c4cc(c(c(c4)OC)OC)OC)C5CCCCC5
Ligand InChI: InChI=1S/C42H54N2O10/c1-49-34-20-18-27(22-35(34)50-2)17-19-32(29-14-11-15-31(23-29)54-26-38(45)46)43-41(47)33-16-9-10-21-44(33)42(48)39(28-12-7-6-8-13-28)30-24-36(51-3)40(53-5)37(25-30)52-4/h11,14-15,18,20,22-25,28,32-33,39H,6-10,12-13,16-17,19,21,26H2,1-5H3,(H,43,47)(H,45,46)/t32-,33+,39+/m1/s1
Release date: 2016-03-23
Human NMT1 in complex with myristoyl-CoA and inhibitor IMP-917 (PDB entry 5O6H)
Macromolecule: Glycylpeptide N-tetradecanoyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.97
Sequence length: 391 residues
Sequence: GPHMEEASKRSYQFWDTQPVPKLGEVVNTHGPVEPDKDNIRQEPYTLPQGFTWDALDLGDRGVLKELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLPQWHCGVRVVSSRKLVGFISAIPANIHIYDTEKKMVEINFLCVHKKLRSKRVAPVLIREITRRVHLEGIFQAVYTAGVVLPKPVGTCRYWHRSLNPRKLIEVKFSHLSRNMTMQRTMKLYRLPETPKTAGLRPMETKDIPVVHQLLTRYLKQFHLTPVMSQEEVEHWFYPQENIIDTFVVENANGEVTDFLSFYTLPSTIMNHPTHKSLKAAYSFYNVHTQTPLLDLMSDALVLAKMKGFDVFNALDLMENKTFLEKLKFGIGDGNLQYYLYNWKCPSMGAEKVGLVLQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.29
R work: 0.16384
R free: 0.19348
Average B factor: 17.134
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 291
Crystal growth procedure: 0.4M Sodium phosphate buffer, 17.5% PEG 3350
Matthews coefficient: 2.28
Solvent content (%): 45.95
Ligand: TETRADECANOYL-COA (MYA)
Ligand formula: C35 H62 N7 O17 P3 S
Ligand molecular weight: 977.89
Ligand SMILES: CCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C35H62N7O17P3S/c1-4-5-6-7-8-9-10-11-12-13-14-15-26(44)63-19-18-37-25(43)16-17-38-33(47)30(46)35(2,3)21-56-62(53,54)59-61(51,52)55-20-24-29(58-60(48,49)50)28(45)34(57-24)42-23-41-27-31(36)39-22-40-32(27)42/h22-24,28-30,34,45-46H,4-21H2,1-3H3,(H,37,43)(H,38,47)(H,51,52)(H,53,54)(H2,36,39,40)(H2,48,49,50)/t24-,28-,29-,30+,34-/m1/s1
Release date: 2018-05-16
Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and inhibitor bound (PDB entry 6FZ3)
Macromolecule: Glycylpeptide N-tetradecanoyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.97
Sequence length: 403 residues
Sequence: MGSSHHHHHHSSGRENLYFQGRSYQFWDTQPVPKLGEVVNTHGPVEPDKDNIRQEPYTLPQGFTWDALDLGDRGVLKELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLPQWHCGVRVVSSRKLVGFISAIPANIHIYDTEKKMVEINFLCVHKKLRSKRVAPVLIREITRRVHLEGIFQAVYTAGVVLPKPVGTCRYWHRSLNPRKLIEVKFSHLSRNMTMQRTMKLYRLPETPKTAGLRPMETKDIPVVHQLLTRYLKQFHLTPVMSQEEVEHWFYPQENIIDTFVVENANGEVTDFLSFYTLPSTIMNHPTHKSLKAAYSFYNVHTQTPLLDLMSDALVLAKMKGFDVFNALDLMENKTFLEKLKFGIGDGNLQYYLYNWKCPSMGAEKVGLVLQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.19865
R free: 0.23492
Average B factor: 27.798
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: 24% PEG 4000
5 mM NiCl2
0.1 M Na citrate
5% Glycerol
Matthews coefficient: 2.16
Solvent content (%): 43.08
Ligand: 2,6-bis(chloranyl)-4-[2-(4-methylpiperazin-1-yl)pyridin-4-yl]-~{N}-(1,3,5-trimethylpyrazol-4-yl)benzenesulfonamide (EBK)
Ligand formula: C22 H26 Cl2 N6 O2 S
Ligand molecular weight: 509.452
Ligand SMILES: Cc1c(c(n(n1)C)C)NS(=O)(=O)c2c(cc(cc2Cl)c3ccnc(c3)N4CCN(CC4)C)Cl
Ligand InChI: InChI=1S/C22H26Cl2N6O2S/c1-14-21(15(2)29(4)26-14)27-33(31,32)22-18(23)11-17(12-19(22)24)16-5-6-25-20(13-16)30-9-7-28(3)8-10-30/h5-6,11-13,27H,7-10H2,1-4H3
Release date: 2019-03-27
A fragment-based inhibitor of SHP2 (PDB entry 8S0K)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 537 residues
Sequence: HMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.84
R work: 0.18131
R free: 0.22788
Average B factor: 41.139
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 0.5M K formate
15% PEG 3350
0.1M pH=8 Bis-Tris propane/HCl
Matthews coefficient: 2.19
Solvent content (%): 43.96
Ligand: 3-[2,3-bis(chloranyl)phenyl]-5-methyl-6-(piperazin-1-ylmethyl)-1H-pyrrolo[3,2-b]pyridine (A1H4S)
Ligand formula: C19 H20 Cl2 N4
Ligand molecular weight: 375.295
Ligand SMILES: Cc1c(cc2c(n1)c(c[nH]2)c3cccc(c3Cl)Cl)CN4CCNCC4
Ligand InChI: InChI=1S/C19H20Cl2N4/c1-12-13(11-25-7-5-22-6-8-25)9-17-19(24-12)15(10-23-17)14-3-2-4-16(20)18(14)21/h2-4,9-10,22-23H,5-8,11H2,1H3
Release date: 2024-03-20
PKCeta kinase domain in complex with compound 11 (PDB entry 8FP3)
Macromolecule: Protein kinase C eta type
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.13
Sequence length: 353 residues
Sequence: GSKESSKEGNGIGVNSSNRLGIDNFEFIRVLGKGSFGKVMLARVKETGDLYAVKVLKKDVILQDDDVECTMTEKRILSLARNHPFLTQLFCCFQTPDRLFFVMEFVNGGDLMFHIQKSRRFDEARARFYAAEIISALMFLHDKGIIYRDLKLDNVLLDHEGHCKLADFGMCKEGICNGVTTATFCGTPDYIAPEILQEMLYGPAVDWWAMGVLLYEMLCGHAPFEAENEDDLFEAILNDEVVYPTWLHEDATGILKSFMTKNPTMRLGSLTQGGEHAILRHPFFKEIDWAQLNHRQIEPPFRPRIKSREDVSNFDPDFIKEEPVLTPIDEGHLPMINQDEFRNFEYVSPELQP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1983
R free: 0.2559
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 286.15
Crystal growth procedure: Well Ingredients:
Precipitant: 21.0 %w/v (10.5 uL of stock 50.0 %w/v) PEG 3350
Salt: 0.7 M (2.1875 uL of stock 8.0 M) lithium nitrate
Buffer: 0.1 M (2.5 uL of stock 1.0 M) MES (pH 6.00)
Organic (non-volatile): 7.0 % w/v (2.1875 uL of stock 80.0 % w/v) Glycerol

[Protien] = 12 mg/ml
Matthews coefficient: 2.4
Solvent content (%): 48.76
Ligand: (3P)-3-{4-[(3R,5S)-3-amino-5-methylpiperidin-1-yl]-6-chloro-7H-pyrrolo[2,3-d]pyrimidin-5-yl}benzonitrile (Y3I)
Ligand formula: C19 H19 Cl N6
Ligand molecular weight: 366.847
Ligand SMILES: CC1CC(CN(C1)c2c3c(c([nH]c3ncn2)Cl)c4cccc(c4)C#N)N
Ligand InChI: InChI=1S/C19H19ClN6/c1-11-5-14(22)9-26(8-11)19-16-15(13-4-2-3-12(6-13)7-21)17(20)25-18(16)23-10-24-19/h2-4,6,10-11,14H,5,8-9,22H2,1H3,(H,23,24,25)/t11-,14+/m0/s1
Release date: 2023-04-05
Specific covalent inhibitor(19) of ERK2 (PDB entry 8AOI)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 368 residues
Sequence: MAHHHHHHMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.602
R work: 0.1618
R free: 0.202
Average B factor: 24.325
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 293
Crystal growth procedure: 0.25M (NH4)2SO4
33% MPEG 2000
0.02M Mercaptoethanol
0.1M pH=7.2 HEPES/NaOH
Matthews coefficient: 2.3
Solvent content (%): 46.52
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: 2022-09-28
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z131833926 (PDB entry 7G8U)
Macromolecule: Transforming protein RhoA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 185 residues
Sequence: SMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQARRG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.44
R work: 0.2239
R free: 0.2937
Average B factor: 55.23
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Tris, 2.6M sodium formate
Matthews coefficient: 2.53
Solvent content (%): 51.31
Ligand: FORMIC ACID (FMT)
Ligand formula: C H2 O2
Ligand molecular weight: 46.025
Ligand SMILES: C(=O)O
Ligand InChI: InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)
Release date: 2023-07-12
Crystal structure of CREBBP bromodomain complexed with CBP019 (PDB entry 5MQK)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 119 residues
Sequence: SMRKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.53
R work: 0.1839
R free: 0.2102
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.15 M KSCN, 20% PEG3350, 10% EG
Matthews coefficient: 2.04
Solvent content (%): 39.83
Ligand: 1-(1-methylindol-3-yl)ethanone (QPR)
Ligand formula: C11 H11 N O
Ligand molecular weight: 173.211
Ligand SMILES: CC(=O)c1cn(c2c1cccc2)C
Ligand InChI: InChI=1S/C11H11NO/c1-8(13)10-7-12(2)11-6-4-3-5-9(10)11/h3-7H,1-2H3
Release date: 2017-04-19
Structure of PIK3CA with covalent inhibitor 22 (PDB entry 7R9Y)
Macromolecule: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.153
Sequence length: 948 residues
Sequence: AGTMVGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTRSMLLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRRISTATPYMNGETSTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVKGRKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEEHANWSVSREAGFSYSHAGLSNRLARDNELRENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECRIMSSAKRPLWLNWENPDIMSELLFQNNEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEVVRNSHTIMQIQCKGGLKGALQFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLFHIDFGHFLDHKKKKFGYKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.85
R work: 0.2473
R free: 0.2875
Average B factor: 109.05
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: PEG6000 8%, 0.6 M sodium formate, 0.1 M CHES pH 9.4, 5 mM TCEP
Matthews coefficient: 2.62
Solvent content (%): 53.03
Ligand: N-[2-(4-{4-[2-amino-4-(difluoromethyl)pyrimidin-5-yl]-6-(morpholin-4-yl)-1,3,5-triazin-2-yl}piperazin-1-yl)-2-oxoethyl]-N-methyl-1-(prop-2-enoyl)piperidine-4-carboxamide (2IX)
Ligand formula: C28 H37 F2 N11 O4
Ligand molecular weight: 629.661
Ligand SMILES: CN(CC(=O)N1CCN(CC1)c2nc(nc(n2)N3CCOCC3)c4cnc(nc4C(F)F)N)C(=O)C5CCN(CC5)C(=O)C=C
Ligand InChI: InChI=1S/C28H37F2N11O4/c1-3-20(42)38-6-4-18(5-7-38)25(44)37(2)17-21(43)39-8-10-40(11-9-39)27-34-24(19-16-32-26(31)33-22(19)23(29)30)35-28(36-27)41-12-14-45-15-13-41/h3,16,18,23H,1,4-15,17H2,2H3,(H2,31,32,33)
Release date: 2022-04-06
CCM2 HHD in complex with MEKK3 NPB1 (PDB entry 4Y5O)
Macromolecule: Malcavernin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 98 residues
Sequence: GSKTISESELSASATELLQDYMLTLRTKLSSQEIQQFAALLHEYRNGASIHEFCINLRQLYGDSRKFLLLGLRPFIPEKDSQHFENFLETIGVKDGRG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.2075
R free: 0.2323
Average B factor: 79.879
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M potassium phosphate and 20% PEG 3350
Matthews coefficient: 2.33
Solvent content (%): 47.2
Release date: 2015-07-01
Crystal structure of human ubiquitin-conjugating enzyme UBCH5C (PDB entry 5EGG)
Macromolecule: Ubiquitin-conjugating enzyme E2 D3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.23
Sequence length: 156 residues
Sequence: MGHHHHHHGMALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDRDKYNRISREWTQKYAM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.76
R work: 0.206
R free: 0.2528
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 2% v/v Tacsimate pH 4.0, 0.1 M Sodium acetate  trihydrate pH 4.6, 16% w/v Polyethylene glycol 3350
Matthews coefficient: 2.14
Solvent content (%): 42.44
Release date: 2016-11-02
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000530a (PDB entry 7GSH)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.88
R work: 0.201
R free: 0.2369
Average B factor: 46.484
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.4
Solvent content (%): 63.78
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2024-01-24
Structure of HIV-1 RT complexed with RNA/DNA hybrid in the RNA hydrolysis mode (PDB entry 6BSH)
Macromolecule: REVERSE TRANSCRIPTASE P66 SUBUNIT
Type: Protein, polypeptide(L)
Source organism: Human immunodeficiency virus type 1 (BRU ISOLATE)
EC number: 2.7.7.7
Sequence length: 558 residues
Sequence: GPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDGTKWRKLVDFRELNKKTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWVPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAASRETKLGKAGYVTNKGRQKVVTLTDTTNQKTELQAIHLALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.649
R work: 0.1892
R free: 0.2273
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: Sodium citrate pH 5.2, CaCl2, PEG400
Matthews coefficient: 3.73
Solvent content (%): 67.03
Ligand: (-)-6-CHLORO-4-CYCLOPROPYLETHYNYL-4-TRIFLUOROMETHYL-1,4-DIHYDRO-2H-3,1-BENZOXAZIN-2-ONE (EFZ)
Ligand formula: C14 H9 Cl F3 N O2
Ligand molecular weight: 315.675
Ligand SMILES: c1cc2c(cc1Cl)C(OC(=O)N2)(C#CC3CC3)C(F)(F)F
Ligand InChI: InChI=1S/C14H9ClF3NO2/c15-9-3-4-11-10(7-9)13(14(16,17)18,21-12(20)19-11)6-5-8-1-2-8/h3-4,7-8H,1-2H2,(H,19,20)/t13-/m0/s1
Release date: 2018-01-03
Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity (PDB entry 7L0N)
Macromolecule: Monoclonal antibody S309 Fab heavy chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 230 residues
Sequence: QVQLVQSGAEVKKPGASVKVSCKASGYPFTSYGISWVRQAPGQGLEWMGWISTYNGNTNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCARDYTRGAWFGESLIGGFDNWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC
Oligomeric state: Hetero 6-mer
Stoichiometry: A2, B1, C1, D1, E1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.78
R work: 0.2904
R free: 0.3247
Average B factor: 86.099
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.09 M Buffer System 3 pH 8.5 contains Tris (base); BICINE
27% Precipitant Mix 2 contains Ethylene glycol and PEG8000
0.1 M Ammonium sulfate
Matthews coefficient: 3.76
Solvent content (%): 67.29
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2021-02-17