PDB-4rac: Aza-acyclic nucleoside phosphonates containing a second phosphona...

ID or keywords:

Entry

Database: PDB / ID: 4rac

Title

Aza-acyclic nucleoside phosphonates containing a second phosphonate group as inhibitors of the human, Plasmodium falciparum and vivax 6-oxopurine phosphoribosyltransferases and their pro-drugs as antimalarial agents

Components

Hypoxanthine-guanine phosphoribosyltransferase

Keywords

TRANSFERASE/TRANSFERASE INHIBITOR / 6-oxopurine phosphoribosyltransferase / 9-[(N-Phosphonoethyl-N-phosphonomethoxyethyl)-2-aminoethyl]guanine /

cytoplasmic / TRANSFERASE-TRANSFERASE INHIBITOR complex

Function / homology

Function and homology information

adenine metabolic process / Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / guanine salvage / hypoxanthine metabolic process / hypoxanthine salvage / cerebral cortex neuron differentiation / positive regulation of dopamine metabolic process / lymphocyte proliferation /

hypoxanthine phosphoribosyltransferase ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Keough, D.T. / Hockova, D. / Janeba, Z. / Wang, T.-H. / Naesens, L. / Edstein, M.D. / Chavchich, M. / Guddat, L.W.

Citation

Journal: J.Med.Chem. / Year: 2015
Title: Aza-acyclic Nucleoside Phosphonates Containing a Second Phosphonate Group As Inhibitors of the Human, Plasmodium falciparum and vivax 6-Oxopurine Phosphoribosyltransferases and Their Prodrugs ...
Authors: Keough, D.T. / Hockova, D. / Janeba, Z. / Wang, T.H. / Naesens, L. / Edstein, M.D. / Chavchich, M. / Guddat, L.W.

History

Deposition	Sep 10, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 7, 2015	Provider: repository / Type: Initial release
Revision 1.1	Feb 11, 2015	Group: Database references
Revision 1.2	Dec 23, 2015	Group: Structure summary
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4rac.cif.gz	341.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4rac.ent.gz	281.5 KB	Display	PDB format
PDBx/mmJSON format	4rac.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ra/4rac ftp://data.pdbj.org/pub/pdb/validation_reports/ra/4rac	HTTPS FTP

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Related structure data

Related structure data	4rabC 4radC 4ranC 4raoC 4raqC C: citing same article (ref.)
Similar structure data	4rad-2 4rao-d 5w8v-d 4rad-1 4ijq-d 4raq-d 4rab-d 5m92-d 1xkh-2 1xkh-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (8)

Deposited unit

A: Hypoxanthine-guanine phosphoribosyltransferase

B: Hypoxanthine-guanine phosphoribosyltransferase

C: Hypoxanthine-guanine phosphoribosyltransferase

D: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

99.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	52.823, 114.801, 67.661
Angle α, β, γ (deg.)	90.00, 98.33, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Hypoxanthine-guanine phosphoribosyltransferase / / HGPRT / HGPRTase Mass: 24481.217 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HPRT1, HPRT / Production host: Escherichia coli (E. coli) References: UniProt: P00492, hypoxanthine phosphoribosyltransferase
#2: Chemical	ChemComp-3L4 / [(2-{[2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl][(E)-2-phosphonoethenyl]amino}ethoxy)methyl]phosphonic acid Mass: 438.270 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₂H₂₀N₆O₈P₂
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.07 Å³/Da / Density % sol: 40.66 %
Crystal grow	Method: vapor diffusion, hanging drop / pH: 8 Details: 1 M sodium/potassium tartrate, 0.2 M NaCl, 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95369 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 1, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95369 Å / Relative weight: 1
Reflection	Resolution: 2.05→41.44 Å / Num. obs: 48031 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASES		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.05→41.44 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 27.04 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.244	2000	4.17 %
R_work	0.1941	-	-
obs	0.1963	47991	95.87 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.05→41.44 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6363	0	119	222	6704

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6647
X-RAY DIFFRACTION	f_angle_d	1.167	8998
X-RAY DIFFRACTION	f_dihedral_angle_d	16.347	2520
X-RAY DIFFRACTION	f_chiral_restr	0.073	1008
X-RAY DIFFRACTION	f_plane_restr	0.004	1123

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.05-2.1004	0.3558	91	0.3226	2108	X-RAY DIFFRACTION	62
2.1004-2.1572	0.3683	133	0.2852	3041	X-RAY DIFFRACTION	89
2.1572-2.2207	0.3502	146	0.269	3364	X-RAY DIFFRACTION	98
2.2207-2.2923	0.3286	149	0.2626	3422	X-RAY DIFFRACTION	100
2.2923-2.3743	0.2974	147	0.2426	3373	X-RAY DIFFRACTION	100
2.3743-2.4693	0.2703	148	0.2334	3420	X-RAY DIFFRACTION	100
2.4693-2.5817	0.2711	149	0.2234	3421	X-RAY DIFFRACTION	100
2.5817-2.7178	0.2869	150	0.2168	3428	X-RAY DIFFRACTION	100
2.7178-2.888	0.2945	147	0.2254	3402	X-RAY DIFFRACTION	100
2.888-3.1109	0.2655	149	0.2076	3432	X-RAY DIFFRACTION	100
3.1109-3.4238	0.2562	147	0.1897	3390	X-RAY DIFFRACTION	99
3.4238-3.919	0.1985	149	0.1681	3397	X-RAY DIFFRACTION	99
3.919-4.9362	0.2031	146	0.1412	3381	X-RAY DIFFRACTION	98
4.9362-41.44	0.1813	149	0.1603	3412	X-RAY DIFFRACTION	98

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.8054	-1.0633	0.8483	3.8115	0.4659	4.1733	-0.0856	0.0396	0.4236	0.4917	-0.0584	-0.6002	-0.0451	0.3211	0.0848	0.279	-0.0224	-0.1138	0.2463	0.0142	0.3458	2.972	28.2904	-12.3393
2	3.4224	1.3585	1.0191	3.5025	-1.2637	3.3139	-0.1393	-0.1879	0.1187	0.1668	0.0762	0.4743	-0.1469	-0.6199	0.0774	0.2067	0.0569	0.0088	0.2854	-0.0513	0.2654	-19.4951	27.7229	-16.1367
3	6.9654	3.9796	-0.9258	8.9993	-2.3548	2.2224	0.0391	0.157	0.3563	0.3241	0.0353	0.6008	-0.2139	-0.3498	-0.2112	0.2891	0.0668	-0.078	0.3374	-0.0698	0.2675	-22.3155	32.3975	-25.63
4	6.3552	1.001	-0.1735	3.6496	-1.7785	2.3077	-0.3125	0.4507	0.5663	-0.1797	0.2427	0.5153	-0.6634	-0.6394	0.076	0.4526	0.148	-0.0765	0.3619	-0.0577	0.3508	-20.6872	42.4032	-23.3277
5	1.7973	-0.4416	0.5993	3.7617	-0.3697	2.7018	-0.0823	0.134	0.2166	0.0453	-0.196	-0.2284	-0.5317	0.0856	0.2017	0.2793	0.0002	-0.0879	0.2322	0.0151	0.282	-5.7513	36.8754	-18.4077
6	3.7983	-0.7005	1.1036	4.6479	-1.5959	3.3691	-0.3993	-0.8038	0.7322	0.9587	0.2392	0.0319	-0.7092	-0.2387	0.1316	0.6434	0.0789	-0.0252	0.3742	-0.0605	0.3219	-8.9126	24.0485	2.7333
7	2.3195	0.4943	0.474	6.3652	-1.3606	4.8046	-0.0695	0.1341	-0.2556	-0.1085	0.0125	-0.5519	0.2544	0.2646	0.0649	0.2536	0.0151	0.0249	0.2299	0.006	0.2815	-0.2229	6.8907	-9.6851
8	3.3154	-1.7015	2.3756	4.0889	0.3611	2.4033	0.3452	0.0322	-0.4062	-0.2072	0.0507	-0.0931	0.7882	0.2208	-0.344	0.4744	0.0063	-0.039	0.2781	0.0637	0.3561	-0.6643	-4.3142	-2.848
9	1.9582	-2.8095	0.056	6.2213	-1.1662	1.9366	0.1712	0.0463	0.1631	0.1891	-0.1127	-0.6469	-0.2112	0.1051	-0.1009	0.4437	-0.0121	-0.1337	0.2948	0.0621	0.3968	5.7217	1.236	2.6523
10	3.4954	0.6465	-1.8021	3.0382	-0.0115	3.869	0.0899	-0.4589	-0.0721	0.993	-0.0056	-0.1144	-0.2906	0.0036	-0.0707	0.6341	0.0514	-0.056	0.3532	0.0131	0.2785	-5.2118	14.4959	7.4964
11	0.7235	0.7181	0.2824	2.1621	-0.714	2.3587	0.0585	0.1479	-0.5962	-0.193	-0.14	0.9153	0.4468	-0.708	0.1376	0.3662	-0.0064	-0.166	0.4585	-0.1246	0.7367	-30.1895	8.6134	-27.0757
12	2.5293	0.6984	1.2373	4.0121	-1.08	2.5623	0.0987	0.1009	-0.2206	-0.1929	-0.1733	-0.2861	0.2426	0.0539	0.0724	0.285	0.0545	0.0068	0.2695	-0.0504	0.2251	-7.6662	16.135	-30.2368
13	2.0818	1.0373	0.0568	2.6603	1.1057	5.7774	-0.3507	-0.0403	-0.084	-0.3608	0.0935	-0.0414	-0.5994	-0.1462	0.0535	0.2288	0.0169	0.0384	0.2245	0.0057	0.2432	-9.0134	25.7767	-36.1973
14	8.5298	-6.6819	-1.1583	5.2374	0.8717	0.3316	-0.8509	0.0907	0.9626	-0.0332	-0.0772	1.3784	-0.8675	-0.208	0.6961	0.7335	0.0201	-0.1428	0.4141	-0.1167	0.9276	-4.5156	32.9887	-41.4378
15	5.8804	0.4228	0.6813	3.5125	-2.1576	3.4903	-0.1139	0.236	0.1215	-0.8087	-0.3361	0.0657	0.0509	-0.1733	0.4678	0.504	0.1538	-0.0418	0.4375	-0.1236	0.2256	-12.942	23.429	-44.9366
16	3.0433	0.084	-0.9741	2.3079	-0.1191	1.1891	-0.045	0.5751	-0.1106	-0.6323	-0.0898	0.6741	-0.0783	-0.2767	0.1233	0.4131	0.0361	-0.1776	0.4559	-0.0716	0.382	-23.7752	16.5033	-36.9612
17	4.7354	1.6171	1.2566	3.4986	-0.3852	0.5532	-0.6388	0.7704	-0.3347	-0.2422	0.3639	0.6261	0.4118	-0.5384	0.3426	0.7836	-0.1275	-0.1616	0.4832	-0.1087	0.6815	-23.9779	-5.5761	-26.0896
18	5.3818	-0.6681	1.3147	3.3313	-0.6553	5.271	0.0586	0.6314	-0.852	-0.6321	-0.2527	-0.0109	1.0121	0.2864	0.2117	0.6196	0.0648	0.0044	0.3503	-0.099	0.3677	-8.1349	-3.8955	-26.8299
19	4.317	-1.2683	-1.8952	5.2169	1.4782	7.9465	-0.0204	-0.4772	-0.5055	-0.2189	0.1042	1.1592	0.182	-0.5469	-0.0605	0.2727	-0.055	0.0078	0.4308	0.0267	0.5101	-25.5818	6.2378	-12.0855
20	2.8888	-0.0517	0.3007	3.4064	0.5187	3.923	-0.1705	-0.3027	-0.321	0.9188	0.1381	0.5334	0.1545	-0.5858	0.0782	0.4014	0.0191	0.1173	0.3608	0.0367	0.3411	-18.9924	5.0791	-3.9354
21	2.7265	0.4701	-0.0734	5.8602	-0.2528	5.026	0.0539	-0.147	-0.349	0.008	-0.0027	1.3675	-0.2472	-1.0235	-0.0691	0.4936	0.0362	0.0795	0.7018	0.0981	0.5551	-19.9489	6.9209	1.4187
22	8.3097	0.3997	2.1888	4.4574	-2.8105	5.2706	0.367	-2.1138	-0.2562	1.5809	0.7109	0.7337	0.0273	-1.0715	-0.6258	0.9107	0.0212	0.1975	1.2178	0.21	0.8636	-19.2229	-5.1519	8.4705
23	4.156	-0.6363	0.1926	3.581	-0.6896	3.2702	-0.2307	-0.9855	-0.8214	0.8446	0.1904	1.2424	1.3153	-0.5359	0.1363	0.7867	-0.189	0.2179	0.686	0.138	0.8475	-25.2689	-7.6477	-2.0591
24	3.6735	-2.3337	-1.5675	4.3325	2.569	6.1052	-0.6691	-0.3354	-1.2991	0.5717	0.2346	1.7943	2.0072	0.0191	0.557	0.993	-0.232	0.097	0.6614	0.0606	1.0193	-28.6934	-10.713	-11.3513
25	3.5177	0.5876	-0.5137	3.3967	-0.7772	3.9357	-0.0723	0.3378	-0.6541	-0.4834	0.0008	0.4347	0.9459	-0.0746	0.0443	0.5505	-0.0628	-0.0036	0.2848	-0.0966	0.5712	-14.2612	-9.8809	-16.9557
26	3.1847	0.8478	-0.8295	2.1246	0.5996	0.75	0.0953	0.4262	-0.9798	-0.2872	-0.2021	0.1141	1.1471	0.3321	0.1003	0.7841	0.1191	-0.0209	0.3485	-0.1126	0.6043	-6.6667	-10.6869	-20.7552

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 37 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 38 through 85 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 86 through 121 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 122 through 152 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 153 through 217 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 4 through 37 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 38 through 85 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 86 through 127 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 128 through 165 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 166 through 216 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 6 through 37 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 38 through 87 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 88 through 116 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 117 through 127 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 128 through 152 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 153 through 217 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 4 through 17 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 18 through 37 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 38 through 56 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 57 through 86 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 87 through 100 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 101 through 127 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 128 through 165 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 166 through 179 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 180 through 197 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 198 through 217 )

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