2NZT.A | HK2 – ASTRID

2NZT.A | HK2

General Structure Information

PDB ID	2nzt
HGNC Gene Label(s)	HK2
Structure Name	crystal structure of human hexokinase ii
Resolution	2.45Å
Reference	AUTH W.M.RABEH,H.ZHU,L.NEDYALKOVA,W.TEMPEL,G.WASNEY,AUTH 2 R.LANDRY,M.VEDADI,C.H.ARROWSMITH,A.M.EDWARDS,AUTH 3 M.SUNDSTROM,J.WEIGELT,A.BOCHKAREV,H.PARKTITL CRYSTAL STRUCTURE OF HUMAN HEXOKINASE IIREF TO BE PUBLISHEDREFN

Variant Set Distributions

ExAC Variants

Number Of Residues	871
Number Of SNVs	192
Number Of Permutations	86165
Optimal Distance Threshold	16.0
K Statistic	0.068
p-value	0.026

COSMIC

Number Of Residues	871
Number Of SNVs	8
Number Of Permutations	4649
Optimal Distance Threshold	53.0
K Statistic	0.464
p-value	0.617

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	192
Number Of COSMIC SNVs	7
Optimal Distance Threshold	21.0
K Statistic	0.105
p-value	0.929

Pathogenic Proximity Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
2:75061761		Q>H	A:18	(0.03, 38.40, 22.11)
2:75061762	COSM1023100	V>L	A:19	(0.19, 35.25, 26.31)
2:75081441		M>V	A:29	(-7.39, 24.12, 22.99)
2:75081442		M>T	A:29	(-7.39, 24.12, 22.99)
2:75081444	rs567201785 COSM1023101	R>C	A:30	(-6.71, 27.11, 28.33)
2:75081445	rs142756990	R>H	A:30	(-6.71, 27.11, 28.33)
2:75081455		D>E	A:33	(-8.16, 19.53, 36.66)
2:75081480	rs372666431 COSM3407996	R>W	A:42	(-16.73, 11.21, 29.02)
2:75081481	rs375609405 COSM1023102	R>Q	A:42	(-16.73, 11.21, 29.02)
2:75081486		R>C	A:44	(-13.99, 3.02, 34.03)
2:75081519	rs555921699	T>A	A:55	(-21.17, -3.78, 24.54)
2:75081532		A>V	A:59	(-17.08, 0.04, 20.98)
2:75081537		V>L	A:61	(-12.63, 1.90, 23.25)
2:75081552		T>A	A:66	(-2.92, -9.29, 23.69)
2:75081553		T>I	A:66	(-2.92, -9.29, 23.69)
2:75081564	rs200036720	S>A	A:70	(3.27, -11.74, 31.78)
2:75081575		D>E	A:73	(9.54, -15.20, 33.88)
2:75081579		T>A	A:75	(12.63, -18.02, 31.76)
2:75094768		G>R	A:78	(17.02, -16.88, 22.44)
2:75094772		E>A	A:79	(17.16, -16.44, 18.79)
2:75094780		A>T	A:82	(12.24, -8.50, 14.51)
2:75094789	rs377756765	L>F	A:85	(5.48, -1.76, 11.12)
2:75094799		T>S	A:88	(8.74, 7.06, 12.63)
2:75094807	rs371320494	R>C	A:91	(13.98, -0.33, 13.59)
2:75094808		R>H	A:91	(13.98, -0.33, 13.59)
2:75094825		V>I	A:97	(17.78, -13.92, 25.43)
2:75094852	rs142433390	E>K	A:106	(23.35, -9.31, 21.78)
2:75094874		A>V	A:113	(12.49, 2.81, 3.98)
2:75094876		I>V	A:114	(8.33, 2.47, 3.95)
2:75094882		E>K	A:116	(3.80, 8.16, 0.77)
2:75094897		G>S	A:121	(-0.51, 0.40, -1.60)
2:75099463		M>V	A:138	(18.82, -12.40, 7.32)
2:75099471		K>N	A:140	(24.02, -7.00, 7.82)
2:75099477	rs2229621	Q>H	A:142	(26.61, -13.49, 7.95)
2:75099524		C>F	A:158	(-5.18, -6.47, 15.82)
2:75100403		S>G	A:166	(-2.87, -10.64, 13.89)
2:75100460	rs530781275	V>I	A:185	(-0.25, -9.97, 9.42)
2:75100476	rs139442407	R>Q	A:190	(4.67, -17.22, 7.19)
2:75100986		I>L	A:203	(6.65, -18.92, 15.80)
2:75101047		N>S	A:223	(6.05, -4.09, 38.80)
2:75101056		I>T	A:226	(0.63, 0.60, 31.77)
2:75101059		G>A	A:227	(1.44, 0.98, 27.82)
2:75101401		S>G	A:234	(-1.78, 7.51, 20.89)
2:75101404	rs369460914	N>D	A:235	(-2.43, 3.41, 22.26)
2:75101416		M>V	A:239	(-2.30, -6.10, 32.58)
2:75101435	rs144438174	I>T	A:245	(-11.28, -10.14, 29.69)
2:75101437		D>N	A:246	(-16.35, -10.80, 28.69)
2:75101440		M>V	A:247	(-14.34, -11.36, 24.23)
2:75101443		V>M	A:248	(-11.02, -14.27, 26.76)
2:75101455		E>K	A:252	(-7.66, -17.96, 35.24)
2:75101461		R>W	A:254	(-2.95, -9.46, 35.22)
2:75101462		R>Q	A:254	(-2.95, -9.46, 35.22)
2:75101489		A>D	A:263	(-11.00, 5.88, 18.94)
2:75101491	rs147035224	F>L	A:264	(-12.22, 8.49, 23.50)
2:75101500	rs553676115	D>N	A:267	(-18.91, 7.78, 19.50)
2:75101507	COSM3583442	S>L	A:269	(-17.74, 11.18, 23.19)
2:75101515	rs141419754	D>N	A:272	(-17.78, 18.64, 24.47)
2:75101521	rs28363006	R>C	A:274	(-13.53, 17.46, 18.27)
2:75101522		R>H	A:274	(-13.53, 17.46, 18.27)
2:75101543		I>T	A:281	(-6.85, 17.75, 11.34)
2:75101558		L>P	A:286	(-5.67, 9.01, 4.99)
2:75101563	rs531793433	P>S	A:288	(-11.80, 10.11, 7.59)
2:75101570	rs575008816	K>R	A:290	(-11.45, 7.43, 12.32)
2:75104315		M>L	A:300	(0.62, 12.60, 12.06)
2:75104317		M>I	A:300	(0.62, 12.60, 12.06)
2:75104321		M>V	A:302	(0.88, 18.42, 17.45)
2:75104323	COSM1632125	M>I	A:302	(0.88, 18.42, 17.45)
2:75104348		V>L	A:311	(-4.08, 30.17, 9.08)
2:75104352		K>T	A:312	(-8.67, 31.22, 12.26)
2:75104366		E>K	A:317	(-6.66, 41.28, 10.57)
2:75104368	rs565854734	E>D	A:317	(-6.66, 41.28, 10.57)
2:75104376		F>S	A:320	(1.49, 36.98, 10.89)
2:75104411	rs35677390	G>S	A:332	(2.74, 20.32, 6.64)
2:75104414		R>C	A:333	(5.49, 23.54, 4.55)
2:75104432		I>V	A:339	(5.96, 22.09, 18.55)
2:75105828	rs367777975	I>V	A:349	(11.80, 34.28, 20.86)
2:75105831	rs147658100	R>W	A:350	(16.97, 33.45, 17.28)
2:75105832	rs571011343	R>Q	A:350	(16.97, 33.45, 17.28)
2:75105837		A>T	A:352	(9.81, 30.91, 16.23)
2:75105840	rs61748096	R>C	A:353	(12.29, 35.77, 13.67)
2:75105841		R>L	A:353	(12.29, 35.77, 13.67)
2:75105853		M>T	A:357	(11.81, 33.10, 8.46)
2:75105855		R>W	A:358	(10.75, 26.83, 7.49)
2:75105856	rs201385411	R>Q	A:358	(10.75, 26.83, 7.49)
2:75105867	rs371669153	D>N	A:362	(9.12, 39.30, 8.88)
2:75105895		T>S	A:371	(3.88, 31.04, 17.72)
2:75105900	rs199992983	R>W	A:373	(1.14, 30.23, 25.18)
2:75105919		S>F	A:379	(1.60, 20.43, 23.94)
2:75105942	rs28363029	A>S	A:387	(-3.81, 12.18, 31.77)
2:75105957	rs145270085	A>T	A:392	(-8.76, 5.64, 34.25)
2:75105958		A>D	A:392	(-8.76, 5.64, 34.25)
2:75105960		V>M	A:393	(-6.07, 2.85, 33.49)
2:75105970	rs575135251	R>L	A:396	(-10.42, -1.16, 36.24)
2:75105996		R>W	A:405	(-3.03, 3.23, 47.54)
2:75106020		D>N	A:413	(8.42, 4.83, 23.32)
2:75107402	rs376768203	R>C	A:426	(3.71, 19.82, 30.30)
2:75107403		R>H	A:426	(3.71, 19.82, 30.30)
2:75107409	rs368670086	H>R	A:428	(5.16, 12.56, 34.41)
2:75107417		V>M	A:431	(-1.44, 11.86, 36.27)
2:75107420	rs148796379	R>W	A:432	(2.42, 11.90, 39.57)
2:75107421		R>Q	A:432	(2.42, 11.90, 39.57)
2:75107423		R>W	A:433	(-2.89, 17.33, 39.39)
2:75107426		L>V	A:434	(-5.97, 13.84, 37.98)
2:75107429	rs572996007	V>M	A:435	(-4.65, 9.79, 40.65)
2:75107432	rs150873116	P>S	A:436	(-3.97, 11.50, 44.43)
2:75107435		G>S	A:437	(-3.72, 7.64, 45.26)
2:75107441	rs555380166	D>N	A:439	(3.07, 5.29, 43.59)
2:75107442		D>G	A:439	(3.07, 5.29, 43.59)
2:75107447		R>C	A:441	(8.98, 4.45, 37.83)
2:75107456	rs573942688 COSM3910678	R>C	A:444	(13.08, 7.02, 28.14)
2:75107457	COSM1291541	R>H	A:444	(13.08, 7.02, 28.14)
2:75107469	COSM1730045	G>A	A:448	(12.25, -0.93, 22.13)
2:75107528	rs368018473	R>C	A:468	(4.76, -30.54, 19.36)
2:75107529	rs140756657	R>H	A:468	(4.76, -30.54, 19.36)
2:75107534		R>C	A:470	(1.03, -31.50, 24.99)
2:75107535		R>H	A:470	(1.03, -31.50, 24.99)
2:75107543		T>A	A:473	(2.76, -38.59, 23.83)
2:75107549		E>Q	A:475	(1.20, -39.17, 17.69)
2:75107553		H>R	A:476	(2.85, -43.20, 20.79)
2:75107566		S>R	A:480	(-4.29, -46.62, 11.68)
2:75107573		Q>K	A:483	(-2.47, -49.53, 13.29)
2:75107616	rs145124653	R>Q	A:497	(-3.92, -69.52, 19.51)
2:75107630	rs199889864 COSM3426692	E>K	A:502	(-3.57, -78.14, 18.85)
2:75107651	COSM576266	V>I	A:509	(-8.51, -65.66, 23.60)
2:75107661		L>Q	A:512	(-14.81, -70.29, 27.34)
2:75107666	COSM3840074	T>S	A:514	(-21.43, -71.58, 27.13)
2:75108859		L>S	A:531	(-28.09, -63.87, 40.53)
2:75108882		R>W	A:539	(-29.39, -55.71, 40.20)
2:75108891		L>V	A:542	(-38.83, -62.11, 39.99)
2:75108897	rs267599464	R>C	A:544	(-43.64, -63.25, 37.58)
2:75108898	rs62642507	R>H	A:544	(-43.64, -63.25, 37.58)
2:75108903		R>W	A:546	(-45.76, -65.18, 30.26)
2:75108904	rs143985245	R>Q	A:546	(-45.76, -65.18, 30.26)
2:75108939		K>E	A:558	(-33.38, -55.10, 46.16)
2:75108942		I>V	A:559	(-29.38, -53.06, 44.25)
2:75108943		I>T	A:559	(-29.38, -53.06, 44.25)
2:75108944		I>M	A:559	(-29.38, -53.06, 44.25)
2:75108955		P>L	A:563	(-19.26, -55.38, 51.75)
2:75108958	rs140795639	Q>R	A:564	(-15.11, -54.47, 51.26)
2:75108962		E>D	A:565	(-15.05, -57.05, 53.50)
2:75109250		F>L	A:575	(-20.97, -67.52, 47.41)
2:75109260	rs375536472	I>T	A:578	(-25.00, -64.31, 47.45)
2:75109274	rs550020237	A>S	A:583	(-33.70, -64.45, 51.27)
2:75109275	rs201342639	A>V	A:583	(-33.70, -64.45, 51.27)
2:75109280		F>L	A:585	(-35.84, -60.56, 46.09)
2:75109294		M>I	A:589	(-41.00, -60.20, 45.90)
2:75109299		M>R	A:591	(-41.82, -65.31, 47.15)
2:75112624		I>V	A:615	(-14.81, -74.30, 37.01)
2:75112635	rs577770670	K>N	A:618	(-9.94, -66.19, 37.21)
2:75112654		A>T	A:625	(-11.92, -63.98, 46.82)
2:75112660	rs369111935	G>C	A:627	(-11.77, -70.14, 47.60)
2:75112672		E>K	A:631	(-13.36, -74.35, 43.36)
2:75112678		V>M	A:633	(-19.55, -71.24, 41.44)
2:75112708		R>W	A:643	(-23.63, -72.83, 54.81)
2:75112709		R>Q	A:643	(-23.63, -72.83, 54.81)
2:75113463	COSM1023109	G>R	A:660	(-27.25, -62.56, 28.77)
2:75113471		M>I	A:662	(-26.89, -62.78, 23.46)
2:75113473		M>T	A:663	(-30.33, -64.39, 25.42)
2:75113478		C>R	A:665	(-31.16, -58.50, 23.19)
2:75113481	rs140604042	G>S	A:666	(-32.88, -61.70, 21.35)
2:75113496		H>Y	A:671	(-31.25, -61.17, 13.08)
2:75113620	rs138539339	T>M	A:680	(-16.17, -52.60, 34.77)
2:75113640	rs372422018	M>V	A:687	(-23.50, -68.34, 18.34)
2:75113641		M>T	A:687	(-23.50, -68.34, 18.34)
2:75113652	rs147295617	R>C	A:691	(-17.33, -77.53, 13.39)
2:75113653	COSM4095848	R>H	A:691	(-17.33, -77.53, 13.39)
2:75113658		V>L	A:693	(-16.42, -75.95, 19.50)
2:75113673		G>R	A:698	(-19.74, -82.12, 17.93)
2:75113686		R>Q	A:702	(-25.35, -72.48, 15.65)
2:75113694		V>M	A:705	(-18.24, -68.71, 22.57)
2:75113710		G>E	A:710	(-9.23, -59.14, 27.71)
2:75113718		G>R	A:713	(-2.29, -59.69, 24.96)
2:75113725		N>S	A:715	(0.39, -63.36, 24.08)
2:75113745	rs140962137	R>C	A:722	(0.83, -52.36, 25.75)
2:75113775		L>F	A:732	(0.34, -50.46, 39.36)
2:75113776	rs146286346	L>H	A:732	(0.34, -50.46, 39.36)
2:75113787		P>S	A:736	(-0.49, -58.25, 37.13)
2:75113788	rs146476722	P>L	A:736	(-0.49, -58.25, 37.13)
2:75113791		G>D	A:737	(-0.57, -59.57, 32.84)
2:75115059		L>P	A:750	(-9.75, -45.67, 30.35)
2:75115074	COSM1752678	R>H	A:755	(-3.66, -41.18, 37.20)
2:75115100		R>C	A:764	(7.14, -34.33, 29.98)
2:75115101	rs527493699	R>H	A:764	(7.14, -34.33, 29.98)
2:75115107		L>Q	A:766	(3.96, -30.37, 29.32)
2:75115116		R>Q	A:769	(2.20, -25.18, 36.85)
2:75115121		R>C	A:771	(2.59, -29.80, 40.15)
2:75115133	rs201434233	R>W	A:775	(-7.24, -35.98, 44.27)
2:75115134	rs185927605	R>Q	A:775	(-7.24, -35.98, 44.27)
2:75115139		K>E	A:777	(-0.80, -39.28, 43.39)
2:75115142		T>S	A:778	(-5.47, -40.58, 43.72)
2:75115146		R>K	A:779	(-5.40, -46.26, 42.10)
2:75115175		Q>E	A:789	(-19.32, -35.22, 32.39)
2:75116378	rs543210991	C>W	A:794	(-22.88, -29.85, 24.74)
2:75116398	rs28363057	R>Q	A:801	(-12.27, -24.56, 35.02)
2:75116407		L>R	A:804	(-11.45, -30.82, 35.95)
2:75116410		Q>R	A:805	(-12.83, -27.95, 39.26)
2:75116419		G>V	A:808	(-10.08, -31.67, 42.61)
2:75116427		S>G	A:811	(-7.67, -26.49, 36.29)
2:75116448		I>V	A:818	(-4.53, -30.65, 27.84)
2:75116466		T>A	A:824	(-10.87, -37.66, 23.48)
2:75116479	rs148653106	R>Q	A:828	(-11.26, -42.14, 18.58)
2:75116508	rs377251320	M>L	A:838	(-16.90, -56.81, 17.22)
2:75116511	COSM3391857	A>S	A:839	(-14.76, -56.97, 13.30)
2:75116514	COSM1192315	A>T	A:840	(-13.36, -60.16, 14.07)
2:75116527	rs2229629	R>K	A:844	(-14.73, -66.89, 12.59)
2:75116531		I>M	A:845	(-20.15, -65.23, 12.21)
2:75116533	COSM3000107	R>Q	A:846	(-18.42, -63.40, 6.41)
2:75116541	COSM1326955	R>C	A:849	(-22.70, -68.65, 9.27)
2:75116542		R>H	A:849	(-22.70, -68.65, 9.27)
2:75116559	rs143752008	K>E	A:855	(-26.96, -59.87, 8.99)
2:75116578		D>G	A:861	(-24.77, -53.52, 28.73)
2:75116590	rs567613723	Y>C	A:865	(-22.29, -48.70, 24.46)
2:75116602	rs377363473	P>L	A:869	(-20.43, -39.25, 24.36)
2:75117925	rs141874180	F>L	A:871	(-17.06, -46.38, 22.97)
2:75117955	rs28363065	D>N	A:881	(-14.57, -48.80, 8.27)
2:75117965		P>L	A:884	(-16.89, -54.30, 4.84)
2:75117968		K>I	A:885	(-17.83, -58.39, 3.17)
2:75117977	COSM1023113	V>A	A:888	(-23.45, -54.64, 12.53)
2:75117986		L>Q	A:891	(-29.92, -53.79, 20.75)
2:75117998		D>G	A:895	(-34.09, -55.25, 30.83)
2:75118001	rs370854369	G>D	A:896	(-30.24, -56.94, 31.57)
2:75118012		G>W	A:900	(-31.51, -64.05, 29.73)
2:75118016		A>V	A:901	(-30.73, -65.83, 32.30)
2:75118024		I>V	A:904	(-30.73, -69.82, 29.25)
2:75118048	rs188009487	R>C	A:912	(-35.02, -80.24, 34.04)
2:75118049	COSM576261	R>H	A:912	(-35.02, -80.24, 34.04)

2NZT.A | HK2.

2NZT.A | HK2

General Structure Information

Variant Set Distributions

Ripley’s K Analysis Plots

Variant Set Comparisons

Pathogenic Proximity Analysis

Mapped Variants

[+] ExAC Missense Variants

[+] COSMIC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
2:75081444	COSM1023101	R>C	A:30	(-6.71, 27.11, 28.33)
2:75081481	COSM1023102	R>Q	A:42	(-16.73, 11.21, 29.02)
2:75094879	COSM3583439	P>S	A:115	(8.11, 4.20, 0.20)
2:75112645	COSM1669094	G>C	A:622	(-11.99, -56.47, 41.68)
2:75113463	COSM1023109	G>R	A:660	(-27.25, -62.56, 28.77)
2:75113668	COSM722456	V>E	A:696	(-17.73, -79.74, 22.59)
2:75115074	COSM1752678	R>H	A:755	(-3.66, -41.18, 37.20)
2:75116527	COSM4985390	R>K	A:844	(-14.73, -66.89, 12.59)