General Structure Information
| PDB ID | 3vzd |
| HGNC Gene Label(s) | SPHK1 |
| Structure Name | crystal structure of sphingosine kinase 1 with inhibitor and adp |
| Resolution | 2.3Å |
| Reference | AUTH Z.WANG,X.MIN,S.H.XIAO,S.JOHNSTONE,W.ROMANOW,D.MEININGER,AUTH 2 H.XU,J.LIU,J.DAI,S.AN,S.THIBAULT,N.WALKERTITL MOLECULAR BASIS OF SPHINGOSINE KINASE 1 SUBSTRATETITL 2 RECOGNITION AND CATALYSIS.REF STRUCTURE V. 21 798 2013REFN ISSN 0969-2126PMID 23602659DOI 10.1016/J.STR.2013.02.025 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 346 |
| Number Of SNVs | 105 |
| Number Of Permutations | 9621 |
| Optimal Distance Threshold | 6.0 |
| K Statistic | 0.01 |
| p-value | 0.191 |
COSMIC
| Number Of Residues | 346 |
| Number Of SNVs | 6 |
| Number Of Permutations | 1 |
| Optimal Distance Threshold | 16.0 |
| K Statistic | 0.067 |
| p-value | 1.0 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 105 |
| Number Of COSMIC SNVs | 6 |
| Optimal Distance Threshold | 25.0 |
| K Statistic | 0.266 |
| p-value | 0.846 |
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 17:74382080 | G>S | A:9 | (-18.25, -15.51, 13.64) | |
| 17:74382089 | P>S | A:12 | (-17.86, -5.89, 12.49) | |
| 17:74382093 | R>P | A:13 | (-22.31, -4.13, 8.08) | |
| 17:74382101 | R>G | A:16 | (-12.17, 0.43, 10.28) | |
| 17:74382102 | R>H | A:16 | (-12.17, 0.43, 10.28) | |
| 17:74382105 | V>A | A:17 | (-9.66, -3.77, 6.46) | |
| 17:74382119 | N>H | A:22 | (2.66, -8.40, -3.86) | |
| 17:74382122 | P>S | A:23 | (2.62, -5.40, -6.21) | |
| 17:74382128 | COSM1716234 | G>S | A:25 | (1.11, -10.25, -8.35) |
| 17:74382135 | rs139585838 | K>T | A:27 | (0.90, -12.30, -13.46) |
| 17:74382136 | K>N | A:27 | (0.90, -12.30, -13.46) | |
| 17:74382153 | L>H | A:33 | (-7.04, -7.59, -9.99) | |
| 17:74382158 | rs541550244 | R>G | A:35 | (-8.29, -0.27, -7.16) |
| 17:74382173 | P>A | A:40 | (-16.09, -2.51, -5.95) | |
| 17:74382188 | A>T | A:45 | (-20.12, -3.88, 2.42) | |
| 17:74382189 | A>V | A:45 | (-20.12, -3.88, 2.42) | |
| 17:74382198 | rs201349077 | S>F | A:48 | (-13.20, 0.39, 5.28) |
| 17:74382216 | T>S | A:54 | (4.05, -6.13, 0.60) | |
| 17:74382304 | R>W | A:56 | (10.76, -5.23, 1.55) | |
| 17:74382319 | R>W | A:61 | (7.50, -12.25, 8.96) | |
| 17:74382367 | V>I | A:77 | (-3.66, -11.20, 2.69) | |
| 17:74382374 | rs570383206 | S>C | A:79 | (-0.96, -12.78, -2.77) |
| 17:74382474 | V>M | A:87 | (1.03, -12.45, 8.26) | |
| 17:74382483 | G>R | A:90 | (4.30, -12.24, 12.82) | |
| 17:74382501 | D>N | A:96 | (1.07, -9.74, 21.68) | |
| 17:74382502 | D>A | A:96 | (1.07, -9.74, 21.68) | |
| 17:74382521 | Q>H | A:102 | (-7.32, -14.14, 18.55) | |
| 17:74382525 | rs201193043 | P>S | A:104 | (-9.48, -11.48, 12.07) |
| 17:74382532 | rs149745954 | C>Y | A:106 | (-8.41, -12.57, 4.52) |
| 17:74382540 | P>S | A:109 | (-6.92, -14.58, -4.57) | |
| 17:74382547 | G>D | A:111 | (-2.02, -15.66, -8.77) | |
| 17:74382891 | E>K | A:127 | (-18.32, -24.35, -8.39) | |
| 17:74382906 | E>K | A:132 | (-10.58, -13.22, -12.33) | |
| 17:74382922 | N>S | A:137 | (-16.00, -16.24, -4.85) | |
| 17:74382928 | rs140394750 | T>M | A:139 | (-14.29, -10.69, -2.09) |
| 17:74382937 | rs145016605 | L>P | A:142 | (-14.61, -10.10, 3.32) |
| 17:74382943 | rs375612286 | R>H | A:144 | (-21.27, -13.30, 2.45) |
| 17:74382946 | R>Q | A:145 | (-18.85, -8.78, 7.38) | |
| 17:74382951 | rs199994196 | L>M | A:147 | (-15.23, -15.44, 11.17) |
| 17:74382957 | rs532940482 | P>A | A:149 | (-11.74, -21.51, 13.51) |
| 17:74382970 | L>Q | A:153 | (1.90, -26.72, 11.42) | |
| 17:74382982 | T>M | A:157 | (14.37, -27.21, 12.08) | |
| 17:74382988 | S>L | A:159 | (18.69, -25.63, 12.88) | |
| 17:74383002 | F>I | A:164 | (4.43, -21.14, 13.18) | |
| 17:74383003 | F>S | A:164 | (4.43, -21.14, 13.18) | |
| 17:74383009 | V>A | A:166 | (-1.19, -21.94, 7.11) | |
| 17:74383021 | A>V | A:170 | (6.56, -30.58, 1.25) | |
| 17:74383023 | W>R | A:171 | (10.69, -35.17, 1.30) | |
| 17:74383041 | V>M | A:177 | (7.89, -29.04, -8.80) | |
| 17:74383047 | L>I | A:179 | (12.37, -25.05, -6.56) | |
| 17:74383051 | rs145677246 | E>G | A:180 | (12.41, -27.59, -10.68) |
| 17:74383053 | S>C | A:181 | (8.17, -24.13, -11.09) | |
| 17:74383054 | S>N | A:181 | (8.17, -24.13, -11.09) | |
| 17:74383069 | R>H | A:186 | (6.37, -16.34, -17.73) | |
| 17:74383080 | M>L | A:190 | (-0.24, -24.12, -16.41) | |
| 17:74383082 | rs186544262 | M>I | A:190 | (-0.24, -24.12, -16.41) |
| 17:74383083 | R>C | A:191 | (3.77, -22.95, -11.70) | |
| 17:74383090 | T>S | A:193 | (1.15, -29.45, -14.96) | |
| 17:74383095 | rs148141598 | G>S | A:195 | (6.62, -29.80, -13.74) |
| 17:74383108 | rs17850292 | R>H | A:199 | (11.40, -34.00, -11.54) |
| 17:74383122 | R>C | A:204 | (14.96, -38.31, -7.18) | |
| 17:74383123 | R>H | A:204 | (14.96, -38.31, -7.18) | |
| 17:74383131 | rs143291987 | R>C | A:207 | (17.80, -42.61, 1.16) |
| 17:74383132 | rs147360809 | R>H | A:207 | (17.80, -42.61, 1.16) |
| 17:74383134 | rs56104262 | G>S | A:208 | (13.78, -41.51, 4.56) |
| 17:74383141 | L>R | A:210 | (7.81, -40.81, 7.97) | |
| 17:74383164 | V>M | A:218 | (-3.79, -39.28, 21.27) | |
| 17:74383207 | G>D | A:232 | (5.43, -19.90, 22.56) | |
| 17:74383212 | V>I | A:234 | (3.95, -25.81, 24.24) | |
| 17:74383213 | V>A | A:234 | (3.95, -25.81, 24.24) | |
| 17:74383222 | H>R | A:237 | (1.95, -34.27, 21.07) | |
| 17:74383269 | COSM3989354 | P>S | A:253 | (8.34, -49.06, 7.14) |
| 17:74383270 | P>L | A:253 | (8.34, -49.06, 7.14) | |
| 17:74383275 | E>K | A:255 | (13.61, -45.85, 4.76) | |
| 17:74383279 | D>G | A:256 | (12.53, -45.02, -0.65) | |
| 17:74383309 | rs149492135 | S>L | A:266 | (-8.88, -29.21, 0.62) |
| 17:74383318 | G>A | A:269 | (-4.76, -25.88, -5.19) | |
| 17:74383320 | S>C | A:270 | (-6.98, -23.92, -7.67) | |
| 17:74383338 | rs571579493 | P>T | A:276 | (-11.31, -35.54, -0.78) |
| 17:74383341 | M>V | A:277 | (-11.03, -37.15, 2.84) | |
| 17:74383342 | M>T | A:277 | (-11.03, -37.15, 2.84) | |
| 17:74383347 | R>C | A:279 | (-13.25, -28.67, 7.36) | |
| 17:74383348 | rs34632043 | R>H | A:279 | (-13.25, -28.67, 7.36) |
| 17:74383354 | A>V | A:281 | (-10.69, -31.53, 12.71) | |
| 17:74383366 | rs151189975 | M>T | A:285 | (-2.56, -32.83, 9.78) |
| 17:74383367 | M>I | A:285 | (-2.56, -32.83, 9.78) | |
| 17:74383368 | H>Y | A:286 | (-5.08, -34.04, 5.70) | |
| 17:74383380 | rs376807879 | V>M | A:290 | (4.23, -41.67, -2.55) |
| 17:74383383 | rs369937899 | R>W | A:291 | (5.32, -47.15, -1.14) |
| 17:74383384 | rs200406718 | R>Q | A:291 | (5.32, -47.15, -1.14) |
| 17:74383387 | COSM984660 | A>V | A:292 | (8.77, -46.23, -3.92) |
| 17:74383398 | COSM307670 | R>C | A:296 | (7.45, -42.64, -14.89) |
| 17:74383399 | rs144131867 | R>H | A:296 | (7.45, -42.64, -14.89) |
| 17:74383401 | A>T | A:297 | (1.59, -43.10, -15.17) | |
| 17:74383413 | R>C | A:301 | (-3.24, -42.31, -14.70) | |
| 17:74383416 | L>F | A:302 | (-2.70, -40.10, -8.79) | |
| 17:74383431 | rs199672053 | E>K | A:307 | (-9.14, -31.26, -11.61) |
| 17:74383440 | R>G | A:310 | (-12.63, -38.35, -9.47) | |
| 17:74383441 | R>K | A:310 | (-12.63, -38.35, -9.47) | |
| 17:74383443 | H>D | A:311 | (-6.74, -38.61, -5.56) | |
| 17:74383453 | Y>C | A:314 | (-7.00, -44.47, -9.53) | |
| 17:74383456 | E>V | A:315 | (-7.87, -48.49, -4.38) | |
| 17:74383461 | rs146794156 | P>S | A:317 | (-0.59, -49.36, -3.50) |
| 17:74383465 | Y>S | A:318 | (3.13, -47.86, -4.68) | |
| 17:74383469 | rs577600312 | L>F | A:319 | (-1.23, -43.07, -1.90) |
| 17:74383476 | COSM4069873 | V>M | A:322 | (-2.91, -40.81, 7.84) |
| 17:74383479 | P>S | A:323 | (-5.33, -39.07, 9.97) | |
| 17:74383488 | A>T | A:326 | (2.22, -35.34, 14.49) | |
| 17:74383509 | rs116933256 | D>N | A:333 | (21.33, -38.59, 2.30) |
| 17:74383518 | rs369049112 | G>S | A:336 | (16.36, -31.25, 2.41) |
| 17:74383527 | A>T | A:339 | (7.72, -26.87, 0.94) | |
| 17:74383537 | COSM1680104 | G>A | A:342 | (5.62, -22.92, -1.06) |
| 17:74383547 | COSM3522541 | M>I | A:345 | (12.70, -25.10, 4.09) |
| 17:74383548 | V>F | A:346 | (16.95, -26.40, 3.32) | |
| 17:74383554 | rs143355437 | E>K | A:348 | (19.60, -32.23, 8.26) |
| 17:74383560 | rs55648239 | V>M | A:350 | (11.21, -31.47, 9.88) |
| 17:74383567 | G>A | A:352 | (5.30, -31.43, 13.88) | |
| 17:74383577 | H>Q | A:355 | (-1.15, -26.13, 17.64) | |
| 17:74383579 | P>L | A:356 | (-6.03, -26.36, 18.04) | |
| 17:74383581 | N>D | A:357 | (-9.15, -23.96, 16.19) | |
| 17:74383582 | rs549686948 COSM1189578 |
N>S | A:357 | (-9.15, -23.96, 16.19) |
| 17:74383592 | W>C | A:360 | (-11.08, -17.16, 14.60) | |
| 17:74383602 | rs201780441 COSM2743292 |
G>S | A:364 | (-18.30, -20.04, 4.70) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 17:74382128 | COSM1716234 | G>S | A:25 | (1.11, -10.25, -8.35) |
| 17:74382331 | COSM1610810 | R>W | A:65 | (7.33, -8.39, 13.97) |
| 17:74382586 | COSM3712450 | A>D | A:124 | (-18.48, -22.34, 1.09) |
| 17:74383376 | COSM1750338 | F>L | A:288 | (-1.48, -37.29, 1.78) |
| 17:74383537 | COSM1680104 | G>V | A:342 | (5.62, -22.92, -1.06) |
| 17:74383582 | COSM1189578 | N>S | A:357 | (-9.15, -23.96, 16.19) |