Receptor
PDB id Resolution Class Description Source Keywords
5OFV 1.5 Å EC: 1.1.1.95 CRYSTAL STRUCTURE OF HUMAN 3-PHOSPHOGLYCERATE DEHYDROGENASE WITH 5-FLUORO-2-METHYLBENZOIC ACID HOMO SAPIENS DEHYDROGENASE SERINE METABOLISM FBDD OXIDOREDUCTASE
Ref.: VALIDATING AND ENABLING PHOSPHOGLYCERATE DEHYDROGEN (PHGDH) AS A TARGET FOR FRAGMENT-BASED DRUG DISCOVE PHGDH-AMPLIFIED BREAST CANCER. ONCOTARGET 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
9TZ B:401;
A:401;
Valid;
Valid;
none;
none;
Kd = 26.2 mM
154.138 C8 H7 F O2 Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5OFW 1.5 Å EC: 1.1.1.95 CRYSTAL STRUCTURE OF HUMAN 3-PHOSPHOGLYCERATE DEHYDROGENASE WITH 3-CHLORO-4-FLUOROBENZAMIDE HOMO SAPIENS DEHYDROGENASE SERINE METABOLISM FBDD OXIDOREDUCTASE
Ref.: VALIDATING AND ENABLING PHOSPHOGLYCERATE DEHYDROGEN (PHGDH) AS A TARGET FOR FRAGMENT-BASED DRUG DISCOVE PHGDH-AMPLIFIED BREAST CANCER. ONCOTARGET 2016
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5OFV Kd = 26.2 mM 9TZ C8 H7 F O2 Cc1ccc(cc1....
2 5OFW Kd = 1.6 mM 9TW C7 H5 Cl F N O c1cc(c(cc1....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5N53 Kd = 2.8 mM 8NB C9 H10 Cl N O2 CC(=O)Nc1c....
2 5NZP Kd = 6.5 mM 9EW C7 H5 N O2 c1ccc2c(c1....
3 5OFV Kd = 26.2 mM 9TZ C8 H7 F O2 Cc1ccc(cc1....
4 5OFW Kd = 1.6 mM 9TW C7 H5 Cl F N O c1cc(c(cc1....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5N53 Kd = 2.8 mM 8NB C9 H10 Cl N O2 CC(=O)Nc1c....
2 5NZP Kd = 6.5 mM 9EW C7 H5 N O2 c1ccc2c(c1....
3 5OFV Kd = 26.2 mM 9TZ C8 H7 F O2 Cc1ccc(cc1....
4 5OFW Kd = 1.6 mM 9TW C7 H5 Cl F N O c1cc(c(cc1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 9TZ; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 9TZ 1 1
2 5RG 0.527778 0.607143
3 FA0 0.435897 0.607143
4 3SK 0.416667 0.722222
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5OFW; Ligand: 9TW; Similar sites found: 321
This union binding pocket(no: 1) in the query (biounit: 5ofw.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4NJS G08 0.00661 0.4487 None
2 3T3C 017 0.01184 0.43338 None
3 3GGU 017 0.01394 0.42631 None
4 5T2Z 017 0.01587 0.42168 None
5 1GHE ACO 0.02188 0.40784 None
6 1V3S ATP 0.02149 0.40712 None
7 2O4N TPV 0.03499 0.40206 None
8 4M73 M72 0.02857 0.41978 0.896861
9 4M73 SAH 0.03167 0.41584 0.896861
10 2PHW MAN MAN MAN BMA MAN MAN MAN 0.007286 0.41968 1.34529
11 2PHF MAN MAN BMA MAN 0.006739 0.41901 1.34529
12 2PHR MAN MAN BMA MAN 0.007056 0.4178 1.34529
13 2AR6 NAG MAN 0.01038 0.41528 1.34529
14 1UKG MMA 0.005447 0.41314 1.34529
15 2PHR MAN MAN 0.007849 0.40996 1.34529
16 2PHW MAN MAN 0.008148 0.40893 1.34529
17 2PHX MAN MAN 0.00784 0.40627 1.34529
18 2PHF MAN MAN 0.009519 0.40531 1.34529
19 5LW0 AR6 0.03063 0.40496 1.34529
20 1Q8O MAN MMA 0.009755 0.40395 1.34529
21 1Q8Q MAN MMA 0.008652 0.40339 1.34529
22 1Q8S MAN MMA 0.008038 0.40292 1.34529
23 2PHU MAN MAN 0.008614 0.40278 1.34529
24 1Q8V MAN MAN 0.008998 0.40162 1.34529
25 2GND MAN 0.01063 0.40005 1.34529
26 4EBZ NAG NAG NAG NAG 0.01126 0.41034 1.41509
27 1TIQ COA 0.01627 0.40752 1.66667
28 5O4J 9KH 0.005584 0.45624 1.79372
29 5O4J SAH 0.005584 0.45624 1.79372
30 5O4J PJL 0.005829 0.45386 1.79372
31 4BV6 FAD 0.03634 0.41654 1.79372
32 4YZC STU 0.04464 0.40707 1.79372
33 1ATL 0QI 0.01443 0.41946 1.9802
34 2VVM FAD 0.004783 0.46177 2.24215
35 4J36 1HR 0.01052 0.4503 2.24215
36 4J36 FAD 0.008501 0.44536 2.24215
37 1YJQ NAP 0.01406 0.43307 2.24215
38 3CZ7 ACO 0.02141 0.41803 2.24215
39 2IYA UDP 0.01842 0.41059 2.24215
40 1BXO PP7 0.03739 0.40975 2.24215
41 1PL6 572 0.04812 0.40318 2.24215
42 1PL6 NAD 0.03083 0.40105 2.24215
43 2RIO ADP 0.02103 0.40087 2.24215
44 4RPO T6C 0.04407 0.40023 2.24215
45 1EBF NAD 0.0004224 0.50076 2.69058
46 5GT9 NAP 0.007429 0.44712 2.69058
47 5D4V SAH 0.004644 0.4464 2.69058
48 5MBX FAD 0.01444 0.44438 2.69058
49 5MBX SP5 0.01444 0.44438 2.69058
50 1D4D FAD 0.01344 0.44275 2.69058
51 1AE1 NAP 0.01685 0.42646 2.69058
52 4MFZ MFK 0.01641 0.42378 2.69058
53 1F0X FAD 0.02058 0.42144 2.69058
54 1X14 NAD 0.00005168 0.42098 2.69058
55 2Y6Q I7T 0.04922 0.41695 2.69058
56 2Y6Q FAD 0.0299 0.41695 2.69058
57 1U1F 183 0.04375 0.41671 2.69058
58 1M2K APR 0.03093 0.40708 2.69058
59 2IV3 UDP 0.02343 0.40531 2.69058
60 1I7A PHE 0.01117 0.40923 2.7027
61 2ZFU SAH 0.009845 0.42644 2.7907
62 4RGQ 1GP 0.03629 0.41481 2.98913
63 2A92 NAI 0.0005261 0.50704 3.13901
64 1UP7 NAD 0.001457 0.47746 3.13901
65 5KVA SAM 0.001912 0.46872 3.13901
66 3WGT QSC 0.01046 0.45305 3.13901
67 3WGT FAD 0.01013 0.45305 3.13901
68 3G5S FAD 0.008286 0.45072 3.13901
69 2O07 MTA 0.007757 0.44101 3.13901
70 2O07 SPD 0.008649 0.44101 3.13901
71 2FK8 SAM 0.006511 0.43681 3.13901
72 1KPG SAH 0.009599 0.42897 3.13901
73 1SQF SAM 0.007917 0.42766 3.13901
74 5JFL NAD 0.03247 0.40744 3.13901
75 1V2F HCI 0.002692 0.40489 3.13901
76 5IBE 69M 0.04656 0.40404 3.13901
77 1D6S MET PLP 0.0315 0.40392 3.13901
78 2W41 ADP 0.01728 0.4035 3.13901
79 1D6S PLP MET 0.03124 0.40309 3.13901
80 1TB3 FMN 0.03078 0.40264 3.13901
81 3WV8 ATP 0.0007355 0.4866 3.21101
82 2VT3 ATP 0.000005904 0.48249 3.25581
83 3JVH HHV 0.03702 0.40644 3.27869
84 1LDN NAD 0.003977 0.45994 3.58744
85 2X6T NAP 0.01459 0.42734 3.58744
86 2CUL FAD 0.02155 0.42409 3.58744
87 3G89 SAM 0.00879 0.41654 3.58744
88 1XCL SAH 0.02567 0.41621 3.58744
89 4CYI ATP 0.01299 0.41614 3.58744
90 4GOX A3P 0.01935 0.41358 3.58744
91 1WP4 NDP 0.02147 0.41345 3.58744
92 1KYQ NAD 0.00007675 0.41238 3.58744
93 4YJK URA 0.004283 0.40995 3.58744
94 4TQG NDP 0.04086 0.40487 3.58744
95 3JSX FAD 0.03241 0.40456 3.58744
96 5A7Y SAH 0.0173 0.40114 3.58744
97 2VZZ SCA 0.01987 0.41557 3.66972
98 1HN4 MJI 0.02451 0.44067 3.81679
99 4JJF N2I 0.0001675 0.53957 4.03587
100 4JJF FE9 0.0001461 0.53957 4.03587
101 2GLX NDP 0.006276 0.44544 4.03587
102 1JQ3 AAT 0.01067 0.43691 4.03587
103 4C3Y FAD 0.02206 0.42918 4.03587
104 4C3Y ANB 0.02649 0.42872 4.03587
105 1DIG NAP 0.01651 0.42845 4.03587
106 1DIG L37 0.01728 0.42845 4.03587
107 3QVP FAD 0.03014 0.42047 4.03587
108 5KKA 6V0 0.02775 0.41366 4.03587
109 3P2E SAH 0.02729 0.4021 4.03587
110 1J0X NAD 0.001834 0.49789 4.4843
111 3CMC NAD 0.02004 0.44902 4.4843
112 5KVS 6XR 0.006547 0.44892 4.4843
113 5KVS NAP 0.004396 0.44747 4.4843
114 5EZ7 FAD 0.01094 0.44367 4.4843
115 1VQW FAD 0.009657 0.44042 4.4843
116 1JG3 ADN 0.004707 0.43993 4.4843
117 2GVC FAD 0.01046 0.43886 4.4843
118 4CNK FAD 0.0181 0.43271 4.4843
119 3SSO SAH 0.02263 0.42963 4.4843
120 3AB1 FAD 0.02424 0.42843 4.4843
121 2FZW NAD 0.04571 0.41518 4.4843
122 4UP3 FAD 0.04286 0.40992 4.4843
123 4X7G NAP 0.01477 0.40819 4.4843
124 4RQU NAD 0.03648 0.40743 4.4843
125 1F76 FMN 0.03473 0.40623 4.4843
126 5BNW 12V 0.04106 0.40457 4.4843
127 5JCM NAD 0.0143 0.45849 4.65632
128 5JCM ISD 0.0143 0.45849 4.65632
129 5JCM FAD 0.01397 0.45849 4.65632
130 1E6E FAD 0.007315 0.44821 4.6875
131 3VPH OXM 0.0002373 0.53405 4.93274
132 1X7D ORN 0.0007806 0.50939 4.93274
133 1X7D NAD 0.000537 0.50846 4.93274
134 3VPH NAD 0.001032 0.49749 4.93274
135 3CIF NAD 0.001122 0.4931 4.93274
136 3CIF G3H 0.001841 0.48932 4.93274
137 2F5Z FAD 0.002615 0.48767 4.93274
138 2DFV NAD 0.002177 0.47454 4.93274
139 3AYI HCI 0.004403 0.47437 4.93274
140 3AYI FAD 0.00427 0.47437 4.93274
141 1ZMD FAD 0.006353 0.45936 4.93274
142 1O6Z NAD 0.003092 0.45671 4.93274
143 2Q7V FAD 0.007915 0.45503 4.93274
144 4TM3 FAD 0.01695 0.45078 4.93274
145 3ICS FAD 0.009664 0.44508 4.93274
146 1XTP SAI 0.007574 0.42963 4.93274
147 4X9M FAD 0.02366 0.42539 4.93274
148 3ICS ADP 0.007628 0.42528 4.93274
149 3GDN FAD 0.02566 0.42404 4.93274
150 3GDN HBX 0.03269 0.42404 4.93274
151 3ABI NAD 0.01934 0.4238 4.93274
152 1ZMD NAI 0.01592 0.42267 4.93274
153 5DP2 NAP 0.03047 0.41051 4.93274
154 3G2O SAM 0.01862 0.40951 4.93274
155 5K52 OCD 0.02301 0.40806 4.93274
156 5ITV NAI 0.04084 0.40527 4.93274
157 1JJE BYS 0.01951 0.40907 4.95496
158 1P1C SAH 0.0003131 0.51216 5.02513
159 2J9D AMP 0.01087 0.41743 5.04202
160 2J9D ADP 0.01442 0.41573 5.04202
161 4EKQ NPO 0.004768 0.43497 5.34759
162 4M52 FAD 0.002548 0.48584 5.38117
163 1LLU NAD 0.003266 0.46927 5.38117
164 4D42 W0I 0.008829 0.45637 5.38117
165 4D42 NAP 0.008829 0.45637 5.38117
166 4OPC FDA 0.02294 0.45499 5.38117
167 4OPC PGT 0.02541 0.45499 5.38117
168 1UWK URO 0.0121 0.44664 5.38117
169 1UWK NAD 0.0121 0.44664 5.38117
170 2PD4 NAD 0.01187 0.44338 5.38117
171 1Q9I FAD 0.02111 0.44132 5.38117
172 1Q9I TEO 0.02111 0.44132 5.38117
173 2PD4 DCN 0.01399 0.439 5.38117
174 1JNR FAD 0.02668 0.43812 5.38117
175 3JV7 NAD 0.008337 0.43702 5.38117
176 5TV6 PML 0.003015 0.43641 5.38117
177 2B9W FAD 0.03199 0.42671 5.38117
178 5TDF 7A3 0.02749 0.40012 5.38117
179 4RC8 STE 0.02601 0.40616 5.40541
180 5G3U FDA 0.003582 0.47023 5.8296
181 5U8U FAD 0.008461 0.46926 5.8296
182 2IID FAD 0.007713 0.46418 5.8296
183 2IID PHE 0.007713 0.46418 5.8296
184 4RDI ATP 0.002174 0.45636 5.8296
185 2WET FAD 0.01443 0.43942 5.8296
186 5G3U ITW 0.02706 0.42644 5.8296
187 5EB4 FAD 0.02842 0.42644 5.8296
188 5EOW FAD 0.02794 0.42146 5.8296
189 3ITJ FAD 0.03841 0.41979 5.8296
190 1N4W FAD 0.04925 0.4135 5.8296
191 3JUQ AJD 0.01024 0.42635 5.94595
192 3JUQ AKD 0.01144 0.42481 5.94595
193 3MWS 017 0.03718 0.40778 6.06061
194 1SIV PSI 0.0368 0.40773 6.06061
195 3HAD NAD 0.0004723 0.53282 6.27803
196 3QFA FAD 0.001623 0.49389 6.27803
197 4YNU FAD 0.01405 0.44036 6.27803
198 5AYV KPL 0.01074 0.43948 6.27803
199 3NKS FAD 0.0185 0.42835 6.27803
200 4MIG G3F 0.02867 0.42801 6.27803
201 5U5G NAP 0.02758 0.41127 6.27803
202 5AYV NAP 0.01987 0.41037 6.27803
203 3DMH GMP 0.03577 0.40178 6.27803
204 3FHI ANP 0.04303 0.40035 6.27803
205 2YVJ NAI 0.006907 0.4332 6.42202
206 5BW4 SAM 0.001856 0.45954 6.72646
207 4POO SAM 0.03441 0.40317 7
208 3Q9N COA 0.002727 0.46212 7.0922
209 2CDC XYS 0.00538 0.48029 7.17489
210 2CDC NAP 0.00538 0.48029 7.17489
211 5T67 JHZ 0.005896 0.46846 7.17489
212 2F1K NAP 0.00219 0.46756 7.17489
213 2CDC XYP 0.009319 0.46661 7.17489
214 5T67 SAH 0.005377 0.46638 7.17489
215 2JHF NAD 0.02598 0.46459 7.17489
216 2HJR APR 0.003269 0.45554 7.17489
217 3ZNN FAD 0.01783 0.44574 7.17489
218 3ZNN 4WL 0.01783 0.44574 7.17489
219 3CGD FAD 0.03181 0.44214 7.17489
220 3CGD NAD 0.03181 0.44214 7.17489
221 3CGD COA 0.03181 0.44214 7.17489
222 1PZG A3D 0.01087 0.44013 7.17489
223 1CF2 NAP 0.007618 0.43693 7.17489
224 1COY FAD 0.03858 0.41843 7.17489
225 5E4R NAP 0.04107 0.40229 7.17489
226 5BV3 M7G 0.02328 0.40221 7.17489
227 1YAG ATP 0.02974 0.4065 7.2
228 1HDC CBO 0.01687 0.41297 7.48031
229 4J4H 1J1 0.0002078 0.55335 7.62332
230 4J4H NAI 0.0002078 0.55335 7.62332
231 1VI2 NAD 0.007359 0.43907 7.62332
232 4MDH NAD 0.01115 0.43355 7.62332
233 1PS9 NAP 0.01547 0.42546 7.62332
234 3TKY SAH 0.01311 0.42203 7.62332
235 1PS9 FAD 0.04054 0.41359 7.62332
236 1O94 ADP 0.003101 0.46007 8.07175
237 4HSU FAD 0.005952 0.45961 8.07175
238 5J60 FAD 0.007043 0.45916 8.07175
239 4GUT FAD 0.007772 0.45443 8.07175
240 1NVM NAD 0.0056 0.45072 8.07175
241 4EIP K2C 0.01938 0.43752 8.07175
242 4EIP FAD 0.01938 0.43752 8.07175
243 4REP FAD 0.03442 0.41766 8.07175
244 1S8G DAO 0.005193 0.42953 8.26446
245 3NCQ ATP 0.009559 0.42573 8.40336
246 2R4J FAD 0.01733 0.44403 8.52018
247 2R4J 13P 0.01733 0.44403 8.52018
248 3FUU ADN 0.009016 0.42238 8.52018
249 1ELI PYC 0.0371 0.41863 8.52018
250 2OYS FMN 0.01535 0.41532 8.67769
251 4J56 FAD 0.001316 0.50275 8.77193
252 3DZ6 M8E 0.01344 0.41424 8.95522
253 1EZ4 NAD 0.0003754 0.50961 8.96861
254 2B3D FAD 0.005446 0.44433 8.96861
255 4IV9 FAD 0.01272 0.43901 8.96861
256 3RLF MAL 0.002758 0.43771 8.96861
257 5W10 CMP 0.02459 0.40224 9.23077
258 3NJ4 NAD 0.008169 0.48892 9.41704
259 1I9G SAM 0.001513 0.46954 9.41704
260 3NJ4 AFX 0.04722 0.44232 9.41704
261 2XIQ MLC 0.02052 0.4182 9.41704
262 5FJN FAD 0.04064 0.41537 9.41704
263 5FJN BE2 0.0446 0.41537 9.41704
264 1H7F C5P 0.01709 0.4068 9.41704
265 4YSX FAD 0.01158 0.44696 9.61539
266 3NDJ JHZ 0.01316 0.44597 9.86547
267 3NDJ SAH 0.01316 0.44597 9.86547
268 2HQM FAD 0.02429 0.43008 10.3139
269 3LXK MI1 0.0257 0.41244 10.3139
270 2Z3Y F2N 0.005739 0.46037 10.7623
271 5JCA NDP 0.009947 0.46458 11.6592
272 5JCA FAD 0.005926 0.46458 11.6592
273 2CDU FAD 0.005842 0.45743 11.6592
274 2CDU ADP 0.003239 0.45019 11.6592
275 2E5V FAD 0.01528 0.43722 11.6592
276 5TCI 79V 0.02817 0.40209 11.6592
277 5BUK FAD 0.03055 0.42224 12.1076
278 1ZQ9 SAM 0.00085 0.47838 13.0045
279 3H8V ATP 0.00007266 0.53509 13.4529
280 5L95 AMP 0.001158 0.4741 13.4529
281 4XB2 HSE 0.004903 0.45726 13.4529
282 4XB2 NDP 0.003041 0.45726 13.4529
283 2WPF FAD 0.002894 0.50918 13.9013
284 2WPF WPF 0.003608 0.50326 13.9013
285 2HQU DUP 0.02183 0.40559 14.0244
286 4XYM COA 0.002371 0.48199 14.3498
287 2V3B FAD 0.02205 0.4249 14.5455
288 3OND NAD 0.003571 0.47887 14.7982
289 3OND ADN 0.003571 0.47887 14.7982
290 2E7Z MGD 0.007475 0.45423 14.7982
291 5M67 NAD 0.003248 0.48205 15.2466
292 5M67 3D1 0.003652 0.4791 15.2466
293 5M67 ADE 0.003982 0.47682 15.2466
294 4B7X NAP 0.01989 0.42238 15.2466
295 2PT9 2MH 0.003076 0.46962 15.2648
296 2PT9 S4M 0.00195 0.46962 15.2648
297 3QV1 NAD 0.003086 0.46288 15.8537
298 1V8B NAD 0.002095 0.48119 16.1435
299 3TWO NDP 0.02813 0.41465 16.1435
300 1JQD SAH 0.005112 0.45366 16.5919
301 1JQD HSM 0.0133 0.42674 16.5919
302 4IX4 ADP 0.01177 0.41853 17.0404
303 3GGO NAI 0.002626 0.48226 19.7309
304 3GGO ENO 0.002626 0.48226 19.7309
305 2JB2 FAD 0.02222 0.42533 19.7309
306 2JB2 PHE 0.02304 0.42533 19.7309
307 5UAV NDP 0.002518 0.47432 20.6278
308 5UAV TFB 0.002518 0.47432 20.6278
309 2B4R AES 0.001469 0.48772 22.4215
310 2B4R NAD 0.001776 0.48453 22.4215
311 4L8V NAP 0.01401 0.4292 22.87
312 1BW9 NAD 0.003853 0.45267 25.1121
313 1C1X NAD 0.007582 0.44196 25.1121
314 1BXG NAD 0.007415 0.44186 25.1121
315 1BXG HCI 0.01678 0.40079 25.1121
316 1C1D PHE 0.01568 0.40023 25.1121
317 2O4C NAD 0.000009907 0.60802 30.0448
318 2XN5 FUN 0.01604 0.40423 31.4286
319 2NAD NAD 0.00001414 0.60522 43.0493
320 5DN9 NAD 0.0000002119 0.70697 43.9462
321 4ZGS NAD 0.000001268 0.64575 47.9821
Pocket No.: 2; Query (leader) PDB : 5OFW; Ligand: 9TW; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5ofw.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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