8DG6

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	peg4k 20-30%

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.507	α = 90
b = 44.955	β = 117.312
c = 63.417	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	150	PIXEL	DECTRIS PILATUS 200K		2020-11-04	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)	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	1.98	50	98.3	0.085	0.087	0.044	0.916	14	3.7		12847

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.98	2.05	87.9		0.2	0.16	0.916	3	2.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1dic	1.986	37.218	12811	662	98.199	0.2	0.1974	0.21	0.2512	0.26	25.135

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]
0.027		-0.02	0.06		-0.044

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	16.386
r_dihedral_angle_6_deg	16.359
r_dihedral_angle_3_deg	15.77
r_dihedral_angle_1_deg	7.97
r_lrange_it	6.44
r_lrange_other	6.418
r_scangle_it	4.412
r_scangle_other	4.41
r_scbond_it	2.895
r_scbond_other	2.894
r_mcangle_it	2.794
r_mcangle_other	2.794
r_mcbond_it	1.962
r_mcbond_other	1.96
r_angle_refined_deg	1.428
r_angle_other_deg	0.485
r_nbd_refined	0.218
r_nbd_other	0.212
r_symmetry_nbd_other	0.2
r_symmetry_xyhbond_nbd_refined	0.189
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.164
r_symmetry_nbd_refined	0.152
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.063
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1595
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms	32

Software

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