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

ID or keywords:

Entry

Database: PDB / ID: 4ran

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-(2-cyanoethyl)-N-(2-phosphonoethyl))-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: 2.549 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_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	4ran.cif.gz	330.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4ran.ent.gz	274.3 KB	Display	PDB format
PDBx/mmJSON format	4ran.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/4ran ftp://data.pdbj.org/pub/pdb/validation_reports/ra/4ran	HTTPS FTP

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Related structure data

Related structure data	4rabC 4racC 4radC 4raoC 4raqC C: citing same article (ref.)
Similar structure data	4raq-d 4rad-1 4rab-d 4rao-d 5w8v-d 6i98-d 4rac-d 5fp1-d 5brn-d 6acn-d 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

99.5 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)	66.090, 95.367, 139.742
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#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-3L6 / (2-{[2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl](3-aminopropyl)amino}ethyl)phosphonic acid Mass: 359.321 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₂H₂₂N₇O₄P
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.25 Å³/Da / Density % sol: 45.3 %
Crystal grow	Method: vapor diffusion, hanging drop Details: 20% PEG 3000, 0.2 M calcium acetate, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95369 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 5, 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: 2.26→41.53 Å / Num. obs: 29382 / % 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: 2.549→20.005 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 27.44 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.2457	1947	6.8 %
R_work	0.1984	-	-
obs	0.2017	29382	97.05 %

Solvent computation

Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.549→20.005 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6295	0	100	24	6419

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6534
X-RAY DIFFRACTION	f_angle_d	0.698	8845
X-RAY DIFFRACTION	f_dihedral_angle_d	14.654	2451
X-RAY DIFFRACTION	f_chiral_restr	0.05	990
X-RAY DIFFRACTION	f_plane_restr	0.003	1122

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 (%)
2.549-2.613	0.3291	122	0.254	1630	X-RAY DIFFRACTION	85
2.613-2.6834	0.3114	127	0.2579	1773	X-RAY DIFFRACTION	92
2.6834-2.7622	0.3075	142	0.2455	1853	X-RAY DIFFRACTION	95
2.7622-2.8511	0.3336	128	0.2603	1840	X-RAY DIFFRACTION	96
2.8511-2.9527	0.3212	139	0.2379	1859	X-RAY DIFFRACTION	97
2.9527-3.0705	0.3335	136	0.2312	1922	X-RAY DIFFRACTION	98
3.0705-3.2098	0.2796	136	0.2473	1915	X-RAY DIFFRACTION	99
3.2098-3.3782	0.2793	142	0.2334	1926	X-RAY DIFFRACTION	99
3.3782-3.5887	0.2554	142	0.2033	1942	X-RAY DIFFRACTION	100
3.5887-3.864	0.2349	144	0.1991	1967	X-RAY DIFFRACTION	100
3.864-4.2495	0.2104	143	0.1726	1949	X-RAY DIFFRACTION	100
4.2495-4.8567	0.2172	145	0.152	1991	X-RAY DIFFRACTION	100
4.8567-6.0901	0.2388	147	0.1807	2010	X-RAY DIFFRACTION	100
6.0901-20.0057	0.1901	154	0.1855	2088	X-RAY DIFFRACTION	99

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	0.0189	-0.0302	-0.0082	0.054	0.0581	0.0778	0.253	0.0045	0.2398	-0.1451	-0.0911	-0.4115	0.1901	0.2616	-0.0001	0.2989	0.0185	-0.0077	0.5986	0.0842	0.5151	-18.3411	-20.4564	2.3747
2	0.203	-0.1276	0.2581	0.4131	0.0761	0.4339	0.2183	0.1427	-0.0033	0.2404	-0.0974	-0.0315	-0.1552	0.0407	0.0008	0.2793	-0.0542	0.0353	0.4447	0.04	0.4137	-25.5337	-10.3647	8.8202
3	0.1142	0.05	-0.088	0.1122	-0.1355	0.0842	-0.0363	0.1705	0.3386	-0.0415	0.0095	0.1292	-0.1968	0.1781	0.0001	0.3692	-0.0158	-0.0471	0.5024	-0.0069	0.5277	-38.0533	-8.7445	14.3197
4	0.0119	-0.0231	0.0049	0.0219	-0.0192	-0.0154	0.0123	-0.2149	0.2186	0.6463	0.1356	0.6137	-0.3752	-0.1457	-0	1.006	0.0147	0.118	0.684	0.0419	0.6483	-33.2884	-12.9195	30.9669
5	0.1597	-0.283	0.0762	0.3933	0.1209	0.6506	-0.1671	-0.055	0.1427	0.4518	0.0498	-0.0636	0.0965	0.2673	-0.0092	0.3663	-0.0066	-0.0334	0.5592	0.0685	0.4939	-20.8197	-15.712	17.5927
6	0.0274	0.01	0.0652	0.0403	0.0251	0.067	-0.2037	-0.1107	-0.1729	0.1229	-0.0568	0.0231	0.2994	0.3892	0	0.6163	0.043	0.0978	0.6391	0.134	0.5849	-17.2014	-16.4544	-9.1645
7	0.2152	-0.3495	0.0318	0.3537	0.0458	0.4533	-0.1176	0.1716	-0.0736	-0.287	0.2604	-0.042	-0.0161	-0.0513	0	0.4673	-0.095	-0.021	0.5139	0.1274	0.4702	-26.7462	-6.3988	-9.666
8	-0.0007	0.0151	-0.0087	0.0042	-0.0161	0.0411	-0.0988	-0.275	-0.3233	0.2484	0.1245	0.42	-0.4041	-0.1884	-0	0.5897	-0.0724	-0.0255	0.5527	0.117	0.5011	-28.3973	3.6682	-8.9221
9	0.0601	-0.0688	-0.1025	0.1763	0.1239	0.3198	0.1763	0.3276	0.0041	0.0483	0.1614	0.0968	-0.3694	-0.1633	0.0496	0.769	-0.1205	-0.1537	0.6416	0.1109	0.4803	-29.0658	10.3301	-16.0365
10	0.0736	-0.0688	-0.2521	0.1015	0.0799	0.2109	-0.1617	0.1902	0.1889	-0.3313	0.0612	0.1936	-0.2817	0.2086	-0.3885	0.7835	-0.1715	0.1008	0.4497	0.1419	0.4384	-20.1749	0.4249	-24.2971
11	0.0393	0.1	0.0745	0.1017	-0.0394	0.068	-0.2399	0.1296	0.1987	-0.201	0.3049	0.0936	-0.1752	0.0588	-0.0001	0.5568	-0.0757	0.0378	0.5355	0.0641	0.4591	-30.3827	-14.7784	-16.0839
12	0.0068	-0.002	-0.0084	0.0009	0.006	0.0094	0.1533	0.1641	0.0214	-0.1149	0.4855	-0.0819	-0.0663	0.1246	-0.0007	0.6061	-0.1162	-0.1825	0.9223	-0.123	1.1229	-36.3901	-24.4766	-21.2831
13	0.0469	-0.0387	0.0299	0.0214	-0.0305	0.0177	0.0564	-0.0168	-0.1382	-0.083	-0.1124	0.7318	-0.2842	-0.5426	-0.0003	1.0282	0.349	-0.0758	0.777	-0.0451	0.9986	-47.0779	16.7294	12.8982
14	0.056	-0.0602	-0.0944	0.0658	0.0857	0.506	-0.0048	-0.0801	0.3997	0.4098	0.0168	0.4328	-0.7434	-0.503	-0.0026	0.5456	0.1084	-0.0343	0.5709	0.0422	0.6975	-40.5853	6.895	11.0249
15	-0.0267	0.0553	-0.0468	0.0202	0.1012	0.0579	-0.225	0.0811	0.0692	0.2059	-0.0327	0.2637	-0.4372	-0.1149	0.0001	0.5032	-0.0717	-0.088	0.4281	0.0531	0.4346	-25.3495	4.7224	15.9222
16	0.0428	-0.0598	-0.0213	0.0622	-0.0135	0.0189	-0.2184	0.0506	0.0433	0.0288	0.1468	0.2094	-0.0297	-0.0801	-0	0.5583	-0.0961	-0.0439	0.4777	-0.0721	0.3796	-18.0911	4.6809	13.28
17	0.023	0.0423	0.1145	0.0269	0.1089	0.208	-0.0823	-0.0117	0.4139	0.7042	-0.079	0.08	-0.6842	0.0182	-0.0001	0.8251	-0.1198	-0.0987	0.5373	-0.0813	0.4922	-25.2056	6.8977	27.8712
18	1.7997	0.5678	-0.8747	0.1769	-0.0763	1.3429	0.4896	0.6118	1.2317	0.4798	-0.1481	0.2365	-1.6107	-0.6513	0.1904	1.0086	-0.0731	-0.088	0.1676	-0.2336	0.2996	-29.4044	15.3203	27.0066
19	0.1246	0.1034	0.0435	0.0522	0.0439	0.1052	-0.2332	-0.4673	0.0776	0.7915	0.2687	-0.0109	-0.6517	-0.7782	0.002	0.5123	0.1674	0.1841	0.6646	0.0094	0.6141	-47.0888	3.2546	21.3405
20	0.0235	-0.0165	0.0005	0.0338	-0.0212	-0.0042	0.1209	-0.1455	0.1288	0.1421	0.0089	-0.0238	-0.2569	-0.4883	0	1.0602	0.4273	-0.0171	0.8335	0.0929	0.9789	-49.8499	17.5245	1.8029
21	0.0377	-0.0362	0.0556	0.0632	-0.023	0.0628	-0.2618	-0.0536	0.3808	-0.2825	0.1072	0.1095	-0.4066	-0.289	0.0001	1.0869	0.0822	-0.1226	0.4922	0.0761	0.7197	-34.3686	20.4469	-1.3007
22	-0.0027	-0.0099	0.0048	0.0441	-0.0228	0.0424	-0.0698	0.3841	0.1062	0.0922	0.134	0.3788	-0.2208	-0.4802	0.0001	0.476	0.0563	-0.1184	0.6776	-0.0038	0.6338	-48.364	-0.4081	-1.8142
23	0.0436	-0.055	-0.0341	0.0657	0.0007	0.0314	0.0423	0.5683	0.3706	-0.1614	-0.0835	0.6176	-0.1257	-0.239	-0.004	0.7798	-0.0528	-0.2358	0.5186	0.0474	0.5227	-43.5621	-2.7417	-10.9191
24	0.0043	-0.0648	-0.0606	0.0828	0.0767	0.0551	-0.2088	0.4775	-0.0933	0.0796	0.1805	0.2542	-0.1912	0.3656	0	0.8715	0.003	-0.1808	0.7811	0.0024	0.6937	-44.2469	-9.3723	-11.8519
25	0.0968	-0.0275	0.0618	0.0331	0.0152	0.0446	-0.174	0.1511	0.1779	-0.3674	0.407	-0.0719	0.0585	-0.339	-0.0001	1.0632	0.0929	-0.3161	1.0209	0.0352	0.8936	-49.4939	2.858	-19.0387
26	0.0168	0.0244	-0.018	0.0176	-0.0176	0.0084	0.1125	0.1075	0.2119	-0.2605	0.081	-0.0096	0.1788	-0.1284	0.0001	1.0086	0.0417	-0.3633	1.1721	0.0772	1.1589	-54.5789	3.9625	-24.3602
27	0.3082	0.0442	0.1149	0.1123	0.0779	0.0588	-0.0651	0.4104	0.2507	-0.1375	0.2808	0.146	0.1057	-0.4345	0.02	0.931	0.3146	-0.8756	0.915	0.1246	0.6131	-54.0013	1.6621	-14.3816
28	0.1197	0.0324	-0.0048	0.0074	-0.0056	-0.002	-0.0131	0.28	-0.1066	-0.2152	0.0852	-0.0451	-0.3014	-0.1083	0.0744	0.8529	0.4398	-0.365	1.4245	0.2697	1.1156	-57.0541	12.0208	-11.4899
29	0.0666	0.1188	0.141	0.2227	0.2776	0.344	0.2325	0.308	0.4458	-0.4247	0.5913	0.1417	-0.581	-0.1316	0.0503	1.0466	0.2126	-0.2469	0.6845	0.0966	0.9546	-42.9128	17.167	-10.4736
30	0.0057	-0.007	0.0052	0.0147	-0.0136	0.0263	-0.1607	-0.093	0.3074	-0.2883	0.1973	0.0632	-0.2182	0.1569	-0.0001	0.9954	0.0389	-0.2273	0.5574	0.1209	0.664	-36.5992	16.8744	-7.2851
31	0.0034	0.0104	0.0052	0.0282	0.0025	0.0072	0.147	0.1449	0.0148	-0.1657	0.0045	0.1968	0.0075	-0.2258	0.0002	1.7331	0.0885	-0.1713	0.9337	0.4413	1.41	-35.2517	27.7799	-14.0677

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 17 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 18 through 70 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 71 through 100 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 101 through 127 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 128 through 217 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 3 through 17 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 18 through 70 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 71 through 85 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 86 through 120 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 121 through 179 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 180 through 208 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 209 through 217 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 4 through 17 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 18 through 56 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 57 through 85 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 86 through 99 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 100 through 139 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 140 through 179 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 180 through 217 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 4 through 17 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 18 through 37 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 38 through 56 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 57 through 85 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 86 through 100 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 101 through 139 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 140 through 152 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 153 through 165 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 166 through 179 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 180 through 197 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 198 through 208 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 209 through 217 )

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