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Receptor
PDB id Resolution Class Description Source Keywords
3PG7 2.19 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE H. SAPIENS NF1 SEC-PH DOMAIN (DEL17 HOMO SAPIENS SEC LIPID BINDING DOMAIN PH DOMAIN LIPID BINDING PROTEIN
Ref.: STRUCTURAL AND BIOCHEMICAL CONSEQUENCES OF NF1 ASSO NONTRUNCATING MUTATIONS IN THE SEC14-PH MODULE OF NEUROFIBROMIN. HUM.MUTAT. V. 32 191 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
POP B:601;
B:602;
Invalid;
Invalid;
none;
none;
submit data
175.959 H2 O7 P2 O[P@@...
PTY A:400;
B:500;
Valid;
Valid;
none;
none;
submit data
734.039 C40 H80 N O8 P CCCCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3PG7 2.19 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE H. SAPIENS NF1 SEC-PH DOMAIN (DEL17 HOMO SAPIENS SEC LIPID BINDING DOMAIN PH DOMAIN LIPID BINDING PROTEIN
Ref.: STRUCTURAL AND BIOCHEMICAL CONSEQUENCES OF NF1 ASSO NONTRUNCATING MUTATIONS IN THE SEC14-PH MODULE OF NEUROFIBROMIN. HUM.MUTAT. V. 32 191 2011
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 2E2X - PEV C39 H78 N O8 P CCCCCCCCCC....
2 3PG7 - PTY C40 H80 N O8 P CCCCCCCCCC....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 2E2X - PEV C39 H78 N O8 P CCCCCCCCCC....
2 3PG7 - PTY C40 H80 N O8 P CCCCCCCCCC....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 2E2X - PEV C39 H78 N O8 P CCCCCCCCCC....
2 3PG7 - PTY C40 H80 N O8 P CCCCCCCCCC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PTY; Similar ligands found: 95
No: Ligand ECFP6 Tc MDL keys Tc
1 8PE 1 1
2 PEH 1 1
3 PEF 1 1
4 PTY 1 1
5 PEV 1 1
6 9PE 0.983051 1
7 LOP 0.865672 0.980769
8 L9Q 0.865672 0.980769
9 6OU 0.865672 0.980769
10 ZPE 0.814286 0.980769
11 HGX 0.80303 0.793103
12 HGP 0.80303 0.793103
13 6PL 0.80303 0.793103
14 PLD 0.80303 0.793103
15 LIO 0.80303 0.793103
16 PC7 0.80303 0.793103
17 PEE 0.8 0.980769
18 GP7 0.773333 0.980769
19 PEK 0.77027 0.980769
20 CD4 0.769231 0.823529
21 P5S 0.75 0.90566
22 PGT 0.746269 0.826923
23 XP5 0.746269 0.793103
24 LHG 0.746269 0.826923
25 3PH 0.714286 0.788462
26 F57 0.714286 0.788462
27 LPP 0.714286 0.788462
28 6PH 0.714286 0.788462
29 7PH 0.714286 0.788462
30 PCW 0.706667 0.779661
31 PX2 0.703125 0.769231
32 7P9 0.703125 0.788462
33 PX8 0.703125 0.769231
34 PCK 0.688312 0.754098
35 CN3 0.684932 0.823529
36 PGW 0.657895 0.811321
37 D3D 0.657895 0.811321
38 PII 0.657534 0.706897
39 CN6 0.657534 0.823529
40 PD7 0.65625 0.788462
41 P50 0.653846 0.90566
42 DR9 0.649351 0.811321
43 PGV 0.649351 0.811321
44 EPH 0.647059 0.980769
45 PSC 0.646341 0.779661
46 PSF 0.642857 0.90566
47 PGK 0.641026 0.781818
48 P6L 0.641026 0.811321
49 44G 0.637681 0.826923
50 8ND 0.636364 0.730769
51 CDL 0.633803 0.75
52 OZ2 0.632911 0.811321
53 D21 0.625 0.773585
54 M7U 0.625 0.788462
55 PIF 0.618421 0.694915
56 DGG 0.617284 0.781818
57 3PE 0.616438 0.884615
58 PIZ 0.607595 0.706897
59 PC1 0.6 0.724138
60 MC3 0.6 0.724138
61 PCF 0.6 0.724138
62 44E 0.6 0.788462
63 PIO 0.594937 0.694915
64 52N 0.594937 0.694915
65 IP9 0.594937 0.706897
66 B7N 0.585366 0.694915
67 PDK 0.577778 0.833333
68 AGA 0.565789 0.792453
69 FAW 0.553846 0.607843
70 L2C 0.553846 0.607843
71 DDR 0.553846 0.607843
72 DGA 0.553846 0.607843
73 PIE 0.541176 0.65
74 T7X 0.539326 0.694915
75 POV 0.535714 0.711864
76 L9R 0.535714 0.711864
77 LP3 0.533333 0.827586
78 LAP 0.533333 0.827586
79 LPC 0.533333 0.827586
80 P3A 0.523256 0.777778
81 NKO 0.492754 0.788462
82 NKN 0.492754 0.788462
83 42H 0.47619 0.813559
84 DLP 0.472527 0.711864
85 CN5 0.468354 0.843137
86 S12 0.447059 0.87037
87 43Y 0.445946 0.758621
88 PC5 0.443038 0.645161
89 NKP 0.435897 0.773585
90 GEL 0.421687 0.942308
91 3PC 0.421687 0.706897
92 PCJ 0.413793 0.672414
93 PGM 0.410256 0.773585
94 DB4 0.407407 0.644068
95 PBU 0.404762 0.644068
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3PG7; Ligand: PTY; Similar sites found with APoc: 179
This union binding pocket(no: 1) in the query (biounit: 3pg7.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 1OGX EQU None
2 3A6T 8OG None
3 6EHH 2GE None
4 4P7X AKG 0.78125
5 4P7X YCP 0.78125
6 2W9S TOP 1.24224
7 2GQR ADP 1.26582
8 3QP8 HL0 1.63043
9 2DDQ HRB 1.87793
10 1SGJ OAA 1.95312
11 2XN5 FUN 1.95312
12 5OMY 9YE 1.95312
13 3WUD GLC GAL 2.20588
14 1IS3 LAT 2.22222
15 3N0Y APC 2.23464
16 1AUA BOG 2.34375
17 1R5L VIV 2.34375
18 4LIT AKG 2.34375
19 5FXD H7Y 2.34375
20 1GQG DCD 2.34375
21 6FXR AKG 2.34375
22 4W9N TCL 2.34375
23 4CNO 9PY 2.38095
24 4NPL AKG 2.4
25 3STD MQ0 2.42424
26 5JSP DQY 2.48756
27 1UW1 ADP 2.5
28 1MH5 HAL 2.6087
29 4YLZ LAT NAG GAL 2.61438
30 3W9R A8S 2.6455
31 4OCT AKG 2.7027
32 4D06 NAR 2.73438
33 3HYW DCQ 2.73438
34 1OS7 AKG 2.73438
35 2GQS ADP 2.95359
36 2ET1 GLV 2.98507
37 4H6B 10X 3.07692
38 2UZ2 BTN 3.07692
39 3SAO NKN 3.125
40 1Q8Y ADE 3.125
41 2JC9 ADN 3.125
42 5OPM DTP 3.125
43 1EYE PMM 3.125
44 3RWP ABQ 3.125
45 3B1Q NOS 3.125
46 5GZZ GSH 3.125
47 5O9W AKG 3.125
48 3PUR 2HG 3.125
49 1J3R 6PG 3.15789
50 2GC0 PAN 3.19149
51 5XQW 8EU 3.22581
52 1OI6 TMP 3.41463
53 2VFT SOR 3.51562
54 5HVJ ANP 3.51562
55 5FQK 6NT 3.51562
56 3PQB VGP 3.51562
57 2JIG PD2 3.57143
58 1NKI PPF 3.7037
59 2AGC DAO 3.7037
60 1A78 TDG 3.73134
61 1DZK PRZ 3.82166
62 5XEG AKG 3.8961
63 3HX3 RET 3.90625
64 1O6U PLM 3.90625
65 1T0S BML 3.90625
66 3O2K DST 3.90625
67 2VWT PYR 3.90625
68 3SI2 PBD 3.90625
69 5UWA 8ND 3.94089
70 1NWW HPN 4.02685
71 1ZZ7 S0H 4.0404
72 5W1E PHB 4.29688
73 3DAK ANP 4.29688
74 2Z77 HE7 4.31655
75 2Z77 NCA 4.31655
76 3E2M E2M 4.32432
77 3WUC GLC GAL 4.37956
78 6GNO XDI 4.44444
79 3WG3 A2G GAL NAG FUC 4.49438
80 5T7I LAT NAG GAL 4.51613
81 3PPQ CHT 4.6875
82 4FFG LBS 4.6875
83 4UHL VFV 4.6875
84 1M3U KPL 4.6875
85 4L4J NAG NAG BMA MAN NAG 4.97738
86 6FE1 V14 5.07812
87 1WPQ 13P 5.07812
88 6B9R 2HE 5.07812
89 6B9T 2HE 5.07812
90 5MBC FMN 5.07812
91 6D61 4AA 5.12821
92 4YGF AZM 5.12821
93 5H9Q TD2 5.16129
94 1ODM ASV 5.46875
95 6FYV 3NG 5.46875
96 2OZ5 7XY 5.46875
97 2D6M LBT 5.66038
98 5M36 9SZ 5.67686
99 3MPB FRU 5.69106
100 1C1L GAL BGC 5.83942
101 5GLT BGC GAL NAG GAL 5.85938
102 5C3R HMU 5.85938
103 5C3R AKG 5.85938
104 4B5W PYR 5.85938
105 3WV6 GAL BGC 5.85938
106 3ZXE PGZ 6.01504
107 3A16 PXO 6.25
108 6EOZ 58K 6.25
109 5OD2 GLC 6.25
110 6EOZ AKG 6.25
111 4Y24 TD2 6.49351
112 4D4U FUC GAL NAG 6.64062
113 4D4U FUC NDG GAL FUC 6.64062
114 4D4U FUC GAL NDG FUC 6.64062
115 4D52 GXL 6.64062
116 4D52 GIV 6.64062
117 5JZJ AN2 6.64062
118 2BS5 BGC GAL FUC 6.66667
119 4RFR RHN 6.89655
120 1SU2 ATP 6.91824
121 4JNJ BTN 6.95652
122 4QDF 30Q 7.03125
123 5OES ADP 7.03125
124 4AMW 5DI 7.03125
125 5VNF VAL THR SER VAL VAL 7.03125
126 4NZF ARB 7.03125
127 1I7E IBS 7.03125
128 5O5Y GLC 7.03125
129 1GUI BGC BGC BGC BGC BGC BGC 7.09677
130 5FS0 5JC 7.109
131 4QCK ASD 7.42188
132 4OJ8 AKG 7.42188
133 4RSE PLM 7.42188
134 3Q60 ATP 7.42188
135 2ZHL NAG GAL GAL NAG 7.43243
136 3OYW TDG 7.46269
137 1MDC PLM 7.57576
138 3NV3 GAL NAG MAN 7.97101
139 5AIG VPR 8
140 2OVW CBI 8.20312
141 1SLT NDG GAL 8.20895
142 2GBB CIT 8.33333
143 5CXI 5TW 8.37438
144 4M1U A2G MBG 8.57143
145 1OLM VTQ 8.59375
146 2B3B GLC 8.59375
147 4OPC PGT 8.98438
148 2W92 NGT 8.98438
149 4OPC FDA 8.98438
150 4OFG PCG 9.02778
151 5NLD LBT 9.35252
152 1SW1 PBE 9.375
153 5OO5 UUA 9.67742
154 4WVW SLT 9.72222
155 5IKR ID8 9.76562
156 1ULE GLA GAL NAG 10
157 4ZU4 4TG 10.1351
158 5A6N U7E 10.1562
159 3ZW2 NAG GAL FUC 10.3448
160 5L8L ADP 10.9375
161 2P7Q GG6 11.2782
162 5H9P TD2 12.0253
163 3KVY URA 12.1094
164 6E08 NAP 12.1094
165 5NCF 8T5 12.3894
166 5KO1 6UY 12.5
167 3TDC 0EU 12.8906
168 3VMG 9CA 13.0435
169 1OBD ATP 13.2812
170 2A9G ARG 13.2812
171 1EB1 ASP TYR GLU PRO ILE PRO GLU GLU ALA PHE 13.2812
172 5FYR INS 15.2344
173 3RMK BML 18.0723
174 2Y69 CHD 20.1183
175 5Z84 CHD 23.1293
176 5W97 CHD 23.1293
177 5Y02 HBX 26.1682
178 1N5S ADL 29.4643
179 2QL9 CIT 41.2371
Pocket No.: 2; Query (leader) PDB : 3PG7; Ligand: PTY; Similar sites found with APoc: 59
This union binding pocket(no: 2) in the query (biounit: 3pg7.bio2) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 1M2Z BOG 1.95312
2 2WA4 069 1.95312
3 5MUA GAL 1.95312
4 2XN3 ID8 1.95312
5 3WLV AZA 1.95312
6 4ZSI 4R1 2.33918
7 3RGA LSB 2.34375
8 4CSD MFU 2.34375
9 1XIM XYL 2.34375
10 3WW2 SF6 2.34375
11 5LX9 OLB 2.34375
12 2R5V HHH 2.34375
13 4Y0X ADP 2.34375
14 5ML3 DL3 2.68456
15 3I4X DST 2.73438
16 4XCB AKG 2.73438
17 2Y5S 78H 2.73438
18 4WGF HX2 2.92683
19 3SAO DBH 3.125
20 1OJK GLC BGC 3.125
21 1OJJ GLC GAL 3.125
22 2JAP J01 3.125
23 3VQ2 LP4 LP5 MYR DAO 3.125
24 6CGN DA 3.125
25 1Z03 OCH 3.125
26 4BCS BTN 3.2
27 4RLT FSE 3.40136
28 5W0N UPU 3.51562
29 3X01 AMP 3.51562
30 1TKK ALA GLU 3.51562
31 6FWH 5LD 3.5533
32 1OFZ FUC 4.29688
33 4GYI ADP 4.29688
34 1WBI BTN 4.65116
35 5TFZ 7BC 4.66667
36 5B09 4MX 4.80769
37 1X0P FAD 4.8951
38 3FW9 SLX 5.07812
39 5UFF 8B7 5.09259
40 4WW8 VD9 5.46875
41 1LRH NLA 5.52147
42 4JH6 FCN 5.7971
43 5E5U 1PS 6.03015
44 5X7Q GLC GLC GLC GLC GLC 6.25
45 4D4U FUC GAL 6.64062
46 5UGW GSH 8
47 1QY1 PRZ 8.62069
48 3BXO UPP 10.0418
49 5DQ8 FLF 10.1562
50 3ZW2 GLA NAG GAL FUC 10.3448
51 3ZW2 GAL FUC 10.3448
52 5NFB 8VT 10.7955
53 5ODT ADP 10.9375
54 4JX1 CAH 12.3894
55 1V9T SIN ALA PRO ALA NIT 12.6506
56 5I0U DCY 17.5
57 5ZCO CHD 23.1293
58 1KJ1 MAN 27.5229
59 1OGZ EQU 36
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