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Structure paper

TitleSAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction.
Journal, issue, pagesJ. Comput. Aided Mol. Des., Vol. 36, Page 291-311, Year 2022
Publish dateJun 2, 2020 (structure data deposition date)
AuthorsGrosjean, H. / Isik, M. / Aimon, A. / Mobley, D. / Chodera, J. / von Delft, F. / Biggin, P.C.
External linksJ. Comput. Aided Mol. Des. / PubMed:35426591
MethodsX-ray diffraction
Resolution1.151 - 1.514 Å
Structure data

PDB-5rjj:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with NCL-00023833
Method: X-RAY DIFFRACTION / Resolution: 1.151 Å

PDB-5rjk:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with NCL-00024661
Method: X-RAY DIFFRACTION / Resolution: 1.21 Å

PDB-5rjl:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with NCL-00024662
Method: X-RAY DIFFRACTION / Resolution: 1.31 Å

PDB-5rjm:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with NCL-00024671
Method: X-RAY DIFFRACTION / Resolution: 1.407 Å

PDB-5rjn:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with NCL-00024673
Method: X-RAY DIFFRACTION / Resolution: 1.435 Å

PDB-5rjo:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with NCL-00023827
Method: X-RAY DIFFRACTION / Resolution: 1.22 Å

PDB-5rjp:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with NCL-00024672
Method: X-RAY DIFFRACTION / Resolution: 1.242 Å

PDB-5rjq:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with NCL-00024665
Method: X-RAY DIFFRACTION / Resolution: 1.35 Å

PDB-5rjr:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z45705015
Method: X-RAY DIFFRACTION / Resolution: 1.27 Å

PDB-5rjs:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z285642082
Method: X-RAY DIFFRACTION / Resolution: 1.37 Å

PDB-5rjt:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z404993336
Method: X-RAY DIFFRACTION / Resolution: 1.169 Å

PDB-5rju:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z57261895
Method: X-RAY DIFFRACTION / Resolution: 1.32 Å

PDB-5rjv:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z57190020
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-5rjw:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z256709556
Method: X-RAY DIFFRACTION / Resolution: 1.514 Å

PDB-5rjx:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z285782452
Method: X-RAY DIFFRACTION / Resolution: 1.291 Å

PDB-5rjy:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z383325512
Method: X-RAY DIFFRACTION / Resolution: 1.25 Å

PDB-5rjz:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z755044716
Method: X-RAY DIFFRACTION / Resolution: 1.275 Å

PDB-5rk0:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z30932204
Method: X-RAY DIFFRACTION / Resolution: 1.24 Å

PDB-5rk1:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1507502062
Method: X-RAY DIFFRACTION / Resolution: 1.271 Å

PDB-5rk2:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z54633859
Method: X-RAY DIFFRACTION / Resolution: 1.235 Å

PDB-5rk3:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1501469697
Method: X-RAY DIFFRACTION / Resolution: 1.31 Å

PDB-5rk4:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z56791867
Method: X-RAY DIFFRACTION / Resolution: 1.284 Å

PDB-5rk5:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z57478994
Method: X-RAY DIFFRACTION / Resolution: 1.243 Å

PDB-5rk6:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z198194394
Method: X-RAY DIFFRACTION / Resolution: 1.241 Å

PDB-5rk7:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z31721097
Method: X-RAY DIFFRACTION / Resolution: 1.304 Å

PDB-5rk8:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z53116498
Method: X-RAY DIFFRACTION / Resolution: 1.272 Å

PDB-5rk9:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z461898648
Method: X-RAY DIFFRACTION / Resolution: 1.48 Å

PDB-5rka:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z126932614
Method: X-RAY DIFFRACTION / Resolution: 1.33 Å

PDB-5rkb:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z2004563941
Method: X-RAY DIFFRACTION / Resolution: 1.279 Å

PDB-5rkc:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z234898257
Method: X-RAY DIFFRACTION / Resolution: 1.24 Å

PDB-5rkd:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z2168282707
Method: X-RAY DIFFRACTION / Resolution: 1.237 Å

PDB-5rke:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z906021418
Method: X-RAY DIFFRACTION / Resolution: 1.291 Å

PDB-5rkf:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1674937530
Method: X-RAY DIFFRACTION / Resolution: 1.264 Å

PDB-5rkg:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1124201124
Method: X-RAY DIFFRACTION / Resolution: 1.282 Å

PDB-5rkh:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z31432917
Method: X-RAY DIFFRACTION / Resolution: 1.252 Å

PDB-5rki:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z198194396
Method: X-RAY DIFFRACTION / Resolution: 1.268 Å

PDB-5rkj:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z373768898
Method: X-RAY DIFFRACTION / Resolution: 1.46 Å

PDB-5rkk:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z275181224
Method: X-RAY DIFFRACTION / Resolution: 1.43 Å

PDB-5rkl:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1545196403
Method: X-RAY DIFFRACTION / Resolution: 1.36 Å

PDB-5rkm:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z2017168803
Method: X-RAY DIFFRACTION / Resolution: 1.28 Å

PDB-5rkn:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z373768900
Method: X-RAY DIFFRACTION / Resolution: 1.23 Å

PDB-5rko:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z30620520
Method: X-RAY DIFFRACTION / Resolution: 1.42 Å

PDB-5rkp:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1079512010
Method: X-RAY DIFFRACTION / Resolution: 1.35 Å

PDB-5rkq:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1545196101
Method: X-RAY DIFFRACTION / Resolution: 1.3 Å

PDB-5rkr:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1432018343
Method: X-RAY DIFFRACTION / Resolution: 1.37 Å

PDB-5rks:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1696844792
Method: X-RAY DIFFRACTION / Resolution: 1.24 Å

PDB-5rkt:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1266933824
Method: X-RAY DIFFRACTION / Resolution: 1.241 Å

PDB-5rku:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z32367954
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-5rkv:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z56877838
Method: X-RAY DIFFRACTION / Resolution: 1.277 Å

PDB-5rkw:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z27678561
Method: X-RAY DIFFRACTION / Resolution: 1.242 Å

PDB-5rkx:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1324080698
Method: X-RAY DIFFRACTION / Resolution: 1.24 Å

PDB-5rky:
PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z1796014543
Method: X-RAY DIFFRACTION / Resolution: 1.38 Å

Chemicals

ChemComp-HH8:
4-bromanyl-1,8-naphthyridine

ChemComp-HOH:
WATER

ChemComp-UUJ:
5-bromo-2-hydroxybenzonitrile

ChemComp-UUG:
(4-bromo-2-methoxyphenyl)methanol

ChemComp-UU1:
2-(4-bromo-1H-pyrazol-1-yl)ethan-1-ol

ChemComp-UUV:
4-bromo-1-(2-methoxyethyl)-1H-pyrazole

ChemComp-1P8:
6-bromo-1,3-dihydro-2H-indol-2-one

ChemComp-UUS:
4-bromo-1-(2-hydroxyethyl)pyridin-2(1H)-one

ChemComp-HHT:
2-(4-bromanyl-2-methoxy-phenyl)ethanoic acid

ChemComp-S9S:
~{N}-[2-(4-fluorophenyl)ethyl]methanesulfonamide

ChemComp-UUP:
N-cyclopropylpyrazolo[1,5-a]pyrimidine-3-carboxamide

ChemComp-UUM:
5-methyl-N-(1-methyl-1H-pyrazol-4-yl)-1,2-oxazole-3-carboxamide

ChemComp-O2D:
2-cyclohexyl-N-(4H-1,2,4-triazol-4-yl)acetamide

ChemComp-UVD:
methyl {4-[(pyridin-4-yl)methyl]phenyl}carbamate

ChemComp-60P:
3-methylthiophene-2-carboxylic acid

ChemComp-UVA:
N-methyl-2-(methylsulfonyl)aniline

ChemComp-UV7:
N-[(1H-pyrazol-4-yl)methyl]acetamide

ChemComp-K0J:
N-ethyl-1H-1,2,3-triazole-4-carboxamide

ChemComp-T0S:
N-[(4-sulfamoylphenyl)methyl]acetamide

ChemComp-UV1:
6-methoxy-1,3,4,5-tetrahydro-2H-1-benzazepin-2-one

ChemComp-UUY:
2-[methyl(pyridin-2-yl)amino]ethan-1-ol

ChemComp-UVV:
3-amino-1,6-dimethylpyridin-2(1H)-one

ChemComp-K1S:
N,N-diethyl-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-amine

ChemComp-UVS:
5-(methoxymethyl)-1,3,4-thiadiazol-2-amine

ChemComp-O1M:
4-(4-fluorophenyl)piperazine-1-carboxamide

ChemComp-UVM:
ethyl morpholine-4-carboxylate

ChemComp-UVJ:
3-(2-methyl-1H-benzimidazol-1-yl)propanamide

ChemComp-UVG:
N,N-dimethyl-1H-pyrazole-4-carboxamide

ChemComp-T6J:
2-[(methylsulfonyl)methyl]-1H-benzimidazole

ChemComp-UWG:
(1S)-1-(1-cyclopentyl-1H-pyrazol-4-yl)ethan-1-ol

ChemComp-UWD:
N-methyl-1-([1,2,4]triazolo[4,3-a]pyridin-3-yl)methanamine

ChemComp-UW7:
(6S)-1-methyl-4,5,6,7-tetrahydro-1H-benzotriazole-6-carboxylic acid

ChemComp-K2G:
5-chloro-2-(propan-2-yl)pyrimidine-4-carboxamide

ChemComp-UVY:
2-(1-ethyl-1H-pyrazol-4-yl)ethan-1-ol

ChemComp-GOJ:
ethyl 1~{H}-pyrazole-4-carboxylate

ChemComp-LPZ:
2-(4-methylphenoxy)-1-(4-methylpiperazin-4-ium-1-yl)ethanone

ChemComp-K2M:
4-(furan-2-carbonyl)piperazine-1-carboxamide

ChemComp-UWY:
N-(1-ethyl-1H-pyrazol-4-yl)cyclopentanecarboxamide

ChemComp-K0P:
N-[(1-ethyl-1H-pyrazol-4-yl)methyl]pyridine-3-carboxamide

ChemComp-UWV:
2-fluoro-N-[(1H-pyrazol-3-yl)methyl]aniline

ChemComp-O0V:
(2S)-2-[(3-fluoropyridin-2-yl)(methyl)amino]propan-1-ol

ChemComp-NUA:
N-(1-ethyl-1H-pyrazol-4-yl)cyclobutanecarboxamide

ChemComp-GX4:
cyclopropyl-[4-(4-fluorophenyl)piperazin-1-yl]methanone

ChemComp-UWS:
6-methyl-2-[(3-methyl-1,2-oxazol-5-yl)methyl]pyridazin-3(2H)-one

ChemComp-UXJ:
2-fluoro-N-[(3-methyl-1H-pyrazol-4-yl)methyl]aniline

ChemComp-O0G:
(2S)-2-[(5-chloro-3-fluoropyridin-2-yl)amino]propan-1-ol

ChemComp-UXG:
1-(diphenylmethyl)azetidin-3-ol

ChemComp-UXD:
(1H-pyrazol-4-yl)(pyrrolidin-1-yl)methanone

ChemComp-UXA:
~{N}-cyclopropyl-1,3-benzodioxole-5-carboxamide

ChemComp-YI6:
2-(4-ethoxyphenyl)ethanoic acid

ChemComp-UX7:
N-(6-methoxy-1,3-benzothiazol-2-yl)cyclopropanecarboxamide

ChemComp-UR1:
3-fluoro-5-methylbenzene-1-sulfonamide

ChemComp-UX1:
1-[(2-fluorophenyl)methyl]-N-methylcyclopropane-1-carboxamide

Source
  • homo sapiens (human)
KeywordsPROTEIN BINDING / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / Fragment-based drug design / SAMPL7

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