1T0L.B | IDH1 – ASTRID

1T0L.B | IDH1

General Structure Information

PDB ID	1t0l
HGNC Gene Label(s)	IDH1
Structure Name	crystal structure of human cytosolic nadp(+)-dependent isocitrate dehydrogenase in complex with nadp, isocitrate, and calcium(2+)
Resolution	2.41Å
Reference	AUTH X.XU,J.ZHAO,Z.XU,B.PENG,Q.HUANG,E.ARNOLD,J.DINGTITL STRUCTURES OF HUMAN CYTOSOLIC NADP-DEPENDENTTITL 2 ISOCITRATE DEHYDROGENASE REVEAL A NOVELTITL 3 SELF-REGULATORY MECHANISM OF ACTIVITYREF J.BIOL.CHEM. V. 279 33946 2004REFN ISSN 0021-9258PMID 15173171DOI 10.1074/JBC.M404298200

Variant Set Distributions

ExAC Variants

Number Of Residues	414
Number Of SNVs	108
Number Of Permutations	32741
Optimal Distance Threshold	12.0
K Statistic	0.065
p-value	0.76

COSMIC

Number Of Residues	414
Number Of SNVs	24
Number Of Permutations	6913
Optimal Distance Threshold	13.0
K Statistic	0.167
p-value	0.016

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	108
Number Of COSMIC SNVs	18
Optimal Distance Threshold	12.0
K Statistic	0.085
p-value	0.156

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
2:209116272		S>P	B:2	(12.69, -54.00, 53.02)
2:209116266		K>Q	B:4	(12.73, -48.02, 58.19)
2:209116260	rs141118556	S>G	B:6	(13.21, -41.38, 54.03)
2:209116254	rs369048275 COSM3576959	G>S	B:8	(13.60, -39.69, 48.01)
2:209116232		G>E	B:15	(22.14, -51.37, 32.09)
2:209116230	rs192514135	D>H	B:16	(24.23, -53.02, 29.65)
2:209116221	rs11554138	T>A	B:19	(27.28, -53.53, 35.13)
2:209116207	rs535551892	W>C	B:23	(22.81, -50.67, 39.31)
2:209116182	rs142923780	F>V	B:32	(15.88, -51.40, 47.70)
2:209116179	rs555882127 COSM209777	P>S	B:33	(17.29, -53.20, 52.69)
2:209116172		V>A	B:35	(16.55, -46.83, 51.86)
2:209116173	COSM1404907	V>M	B:35	(16.55, -46.83, 51.86)
2:209116164	rs374907791	D>N	B:38	(10.59, -41.31, 44.89)
2:209113382		Y>C	B:42	(13.98, -43.59, 33.45)
2:209113379		D>A	B:43	(16.10, -49.83, 31.05)
2:209113362	COSM1631779	R>C	B:49	(19.26, -47.93, 24.61)
2:209113347		D>N	B:54	(17.46, -43.42, 22.43)
2:209113322		E>A	B:62	(14.48, -33.80, 30.83)
2:209113323	rs144593536	E>K	B:62	(14.48, -33.80, 30.83)
2:209113305		N>D	B:68	(17.87, -32.25, 41.13)
2:209113296	rs73070954	V>I	B:71	(22.08, -43.08, 39.77)
2:209113280		I>T	B:76	(26.34, -51.00, 25.34)
2:209113260	rs565065820	V>F	B:83	(24.01, -53.70, 15.02)
2:209113253		E>G	B:85	(25.43, -58.70, 19.52)
2:209113243	COSM1482708	L>F	B:88	(20.42, -52.80, 16.85)
2:209113230		K>E	B:93	(24.18, -41.16, 19.34)
2:209113221		N>H	B:96	(26.84, -41.16, 28.68)
2:209113210	rs142883642	I>M	B:99	(22.73, -37.49, 29.73)
2:209113188	rs375658806	V>I	B:107	(32.87, -35.11, 34.97)
2:209113176		A>T	B:111	(40.47, -42.45, 43.20)
2:209113173	rs148542200	I>V	B:112	(38.38, -45.36, 45.41)
2:209113158		I>V	B:117	(46.11, -51.56, 47.35)
2:209113155	rs371567806	P>S	B:118	(49.76, -51.75, 45.76)
2:209113151	COSM242544	R>Q	B:119	(50.79, -46.66, 44.18)
2:209113152	COSM1015578	R>W	B:119	(50.79, -46.66, 44.18)
2:209113142		S>N	B:122	(55.75, -44.65, 42.52)
2:209113140	COSM96922	G>R	B:123	(54.38, -41.18, 43.58)
2:209113134		V>L	B:125	(51.31, -40.01, 47.86)
2:209113119	COSM1404902	I>V	B:130	(40.22, -35.48, 36.33)
2:209113098		D>N	B:137	(34.42, -31.47, 21.38)
2:209110124		P>S	B:147	(33.10, -41.50, -1.51)
2:209110117		P>L	B:149	(37.26, -38.23, -5.98)
2:209110118		P>T	B:149	(37.26, -38.23, -5.98)
2:209110091		P>S	B:158	(26.15, -15.34, 9.80)
2:209110082	rs148190775	G>R	B:161	(23.75, -11.26, 7.62)
2:209110066		T>I	B:166	(33.81, -21.04, 2.67)
2:209108325		G>A	B:175	(40.12, -41.09, -3.61)
2:209108319	rs149205273	G>D	B:177	(37.76, -41.31, 3.15)
2:209108317	rs34218846	V>I	B:178	(37.40, -39.82, 6.47)
2:209108307		G>V	B:181	(32.86, -32.02, 12.68)
2:209108303		M>I	B:182	(34.45, -30.79, 16.12)
2:209108301	rs34599179	Y>C	B:183	(30.07, -28.04, 18.65)
2:209108302		Y>H	B:183	(30.07, -28.04, 18.65)
2:209108284	rs62193615	I>V	B:189	(34.30, -23.02, 27.73)
2:209108269		H>Y	B:194	(33.75, -20.23, 36.74)
2:209108256	rs374340555	Q>R	B:198	(34.75, -23.12, 42.15)
2:209108251	rs370342586	A>S	B:200	(40.95, -25.83, 43.69)
2:209108245		S>A	B:202	(37.81, -26.71, 47.80)
2:209108238		G>V	B:204	(44.01, -26.57, 48.00)
2:209108229		L>W	B:207	(44.28, -25.73, 38.21)
2:209108226	rs186787509	Y>C	B:208	(48.12, -27.91, 36.64)
2:209108227		Y>H	B:208	(48.12, -27.91, 36.64)
2:209108208		T>S	B:214	(50.40, -25.35, 19.25)
2:209108190	rs142801125	D>G	B:220	(42.48, -25.55, 21.82)
2:209108184		R>H	B:222	(37.81, -18.85, 23.01)
2:209108185		R>C	B:222	(37.81, -18.85, 23.01)
2:209108158		Y>H	B:231	(43.51, -17.02, 37.53)
2:209106862		K>Q	B:236	(45.62, -14.36, 40.43)
2:209106854		Q>H	B:238	(40.45, -16.38, 45.53)
2:209106837		I>S	B:244	(47.08, -22.17, 45.15)
2:209106832	rs373048968	Y>H	B:246	(45.84, -21.76, 35.73)
2:209106814		D>N	B:252	(52.53, -33.23, 25.15)
2:209106811	rs201394139	D>N	B:253	(54.15, -31.17, 29.70)
2:209106801		A>V	B:256	(54.52, -36.32, 31.94)
2:209106802	COSM1614214	A>S	B:256	(54.52, -36.32, 31.94)
2:209106780		G>E	B:263	(50.11, -35.32, 43.35)
2:209106777		G>A	B:264	(47.83, -32.79, 44.26)
2:209106772	rs199793362	I>V	B:266	(42.73, -29.98, 40.17)
2:209106750	rs369039979	D>G	B:273	(41.93, -35.41, 26.97)
2:209106748		G>S	B:274	(39.18, -37.11, 30.23)
2:209106742		V>M	B:276	(41.65, -41.17, 27.80)
2:209106735		S>L	B:278	(40.27, -41.20, 33.65)
2:209106736	rs201822210	S>P	B:278	(40.27, -41.20, 33.65)
2:209106733		D>H	B:279	(40.56, -44.96, 32.27)
2:209106729		S>F	B:280	(45.38, -43.98, 33.07)
2:209104706	rs141630472	M>T	B:291	(37.28, -43.86, 39.70)
2:209104703	rs62193614	T>I	B:292	(34.68, -41.42, 41.75)
2:209104698		V>M	B:294	(30.17, -36.73, 39.79)
2:209104661	rs138458978	E>A	B:306	(29.11, -42.16, 36.27)
2:209104650		G>R	B:310	(32.22, -50.28, 31.86)
2:209104637	COSM4090677	R>H	B:314	(37.49, -58.16, 28.08)
2:209104635		H>D	B:315	(34.95, -59.85, 33.25)
2:209104629		R>C	B:317	(31.20, -62.26, 26.29)
2:209104625	rs377475055	M>T	B:318	(34.22, -64.86, 31.28)
2:209104602	rs185564694	S>P	B:326	(36.27, -61.17, 39.79)
2:209104598		T>I	B:327	(33.68, -57.91, 38.63)
2:209103946		A>S	B:335	(27.19, -44.04, 42.55)
2:209103935		R>S	B:338	(29.88, -39.86, 46.38)
2:209103927		A>D	B:341	(24.64, -37.67, 49.58)
2:209103912		L>P	B:346	(19.47, -31.18, 48.37)
2:209103897		E>G	B:351	(18.60, -40.75, 59.07)
2:209103889	rs536880332	F>V	B:354	(25.18, -42.46, 59.29)
2:209103882		A>V	B:356	(26.22, -42.97, 52.63)
2:209103862		S>A	B:363	(33.65, -50.65, 51.10)
2:209103859	rs372711897	I>V	B:364	(37.34, -48.79, 52.38)
2:209103855		E>V	B:365	(36.15, -50.99, 56.74)
2:209103849	rs200591678	I>T	B:367	(39.24, -54.03, 50.56)
2:209103850		I>V	B:367	(39.24, -54.03, 50.56)
2:209103843		A>V	B:369	(40.52, -56.78, 55.84)
2:209103834		M>T	B:372	(40.22, -58.40, 47.73)
2:209103831		T>N	B:373	(38.11, -58.35, 43.76)
2:209103816		A>V	B:378	(47.02, -58.18, 41.53)
2:209103800	rs141895800	L>F	B:383	(48.52, -61.46, 37.59)
2:209103798		P>L	B:384	(51.61, -63.68, 37.76)
2:209103796		N>D	B:385	(52.12, -64.66, 41.68)
2:209101885	rs566072712	R>H	B:388	(39.90, -68.52, 44.09)
2:209101852		D>G	B:399	(27.53, -61.91, 49.95)
2:209101853		D>H	B:399	(27.53, -61.91, 49.95)
2:209101846		L>P	B:401	(30.09, -55.79, 51.03)

1T0L.B | IDH1.

1T0L.B | IDH1

General Structure Information

Variant Set Distributions

Ripley’s K Analysis Plots

Variant Set Comparisons

Mapped Variants

[+] ExAC Missense Variants

[+] COSMIC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
2:209116260	COSM1581045	S>G	B:6	(13.21, -41.38, 54.03)
2:209116217	COSM1581044	R>Q	B:20	(21.40, -54.92, 33.83)
2:209116179	COSM209777	P>S	B:33	(17.29, -53.20, 52.69)
2:209113362	COSM1631779	R>C	B:49	(19.26, -47.93, 24.61)
2:209113298	COSM96531	G>D	B:70	(21.49, -39.41, 39.52)
2:209113295	COSM1404906	V>A	B:71	(22.08, -43.08, 39.77)
2:209113296	COSM96923	V>I	B:71	(22.08, -43.08, 39.77)
2:209113217	COSM1669702	G>D	B:97	(26.18, -37.72, 25.75)
2:209113210	COSM53043	I>M	B:99	(22.73, -37.49, 29.73)
2:209113208	COSM88208	R>Q	B:100	(27.79, -36.48, 29.68)
2:209113202	COSM1254583	I>T	B:102	(20.62, -32.42, 27.91)
2:209113164	COSM3708114	K>E	B:115	(45.53, -47.61, 53.79)
2:209113140	COSM96922	G>R	B:123	(54.38, -41.18, 43.58)
2:209113125	COSM1614217	I>V	B:128	(45.11, -37.11, 40.71)
2:209113117	COSM96532	I>M	B:130	(40.22, -35.48, 36.33)
2:209113119	COSM1404902	I>V	B:130	(40.22, -35.48, 36.33)
2:209113111	COSM1169216	R>S	B:132	(35.10, -35.56, 30.92)
2:209113112	COSM28746	R>H	B:132	(35.10, -35.56, 30.92)
2:209113113	COSM28747	R>C	B:132	(35.10, -35.56, 30.92)
2:209113110	COSM86993	RH>HH	B:133	(33.99, -29.79, 29.14)
2:209113106	COSM96534	A>D	B:134	(30.77, -32.67, 29.50)
2:209108317	COSM97131	V>I	B:178	(37.40, -39.82, 6.47)
2:209108226	COSM1614216	Y>C	B:208	(48.12, -27.91, 36.64)
2:209106802	COSM1614214	A>S	B:256	(54.52, -36.32, 31.94)
2:209106786	COSM1669701	S>L	B:261	(53.72, -36.57, 40.22)
2:209106777	COSM4383632	G>D	B:264	(47.83, -32.79, 44.26)
2:209104618	COSM1752297	Q>H	B:320	(27.83, -65.54, 28.23)
2:209104604	COSM1404899	T>M	B:325	(33.34, -63.75, 37.52)