8D95

Scaffold Hopping via Ring Opening Enables Identification of Acyclic Compounds as New Complement Factor D Inhibitors

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DIC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.8	300	PEG 6k

Crystal Properties
Matthews coefficient	Solvent content
1.97	37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.302	α = 90
b = 44.8	β = 114.392
c = 62.132	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	170	PIXEL	DECTRIS PILATUS 200K		2021-04-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.16	50	97.1	0.068	0.071	0.079	0.039	0.965	3.6	3.4		30307

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.32	84.4		0.133	0.116	0.114	0.965	20	2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1DIC	2.166	35.189	9227	510	89.141	0.205	0.2018	0.2629	30.734

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.081		0.019	-0.057		-0.029

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	15.299
r_dihedral_angle_6_deg	15.258
r_dihedral_angle_3_deg	14.689
r_dihedral_angle_1_deg	7.995
r_lrange_it	7.582
r_lrange_other	7.577
r_scangle_it	4.186
r_scangle_other	4.184
r_mcangle_it	3.816
r_mcangle_other	3.814
r_scbond_it	2.811
r_scbond_other	2.809
r_mcbond_it	2.348
r_mcbond_other	2.342
r_chiral_restr_other	2.169
r_angle_refined_deg	1.402
r_angle_other_deg	0.701
r_symmetry_xyhbond_nbd_refined	0.267
r_nbd_refined	0.211
r_symmetry_nbd_refined	0.207
r_nbd_other	0.203
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.161
r_xyhbond_nbd_refined	0.148
r_symmetry_xyhbond_nbd_other	0.091
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.057
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1687
Nucleic Acid Atoms
Solvent Atoms	56
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
SCALEPACK	data scaling
PHASER	phasing