Receptor
PDB id Resolution Class Description Source Keywords
4V24 1.8 Å EC: 2.7.1.91 SPHINGOSINE KINASE 1 IN COMPLEX WITH PF-543 HOMO SAPIENS TRANSFERASE SPHK1 SPHINGOSINE KINASE
Ref.: CRYSTAL STRUCTURE OF SPHINGOSINE KINASE 1 WITH PF-5 ACS MED.CHEM.LETT. V. 5 1329 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GYR A:1450;
B:1450;
Valid;
Valid;
none;
none;
Ki = 4.3 nM
465.604 C27 H31 N O4 S Cc1cc...
ACT A:1451;
Invalid;
none;
submit data
59.044 C2 H3 O2 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4V24 1.8 Å EC: 2.7.1.91 SPHINGOSINE KINASE 1 IN COMPLEX WITH PF-543 HOMO SAPIENS TRANSFERASE SPHK1 SPHINGOSINE KINASE
Ref.: CRYSTAL STRUCTURE OF SPHINGOSINE KINASE 1 WITH PF-5 ACS MED.CHEM.LETT. V. 5 1329 2014
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3VZC - UUL C15 H11 Cl N2 O S c1cc(ccc1c....
2 3VZD - UUL C15 H11 Cl N2 O S c1cc(ccc1c....
3 3VZB - SQS C18 H37 N O2 CCCCCCCCCC....
4 4V24 Ki = 4.3 nM GYR C27 H31 N O4 S Cc1cc(cc(c....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3VZC - UUL C15 H11 Cl N2 O S c1cc(ccc1c....
2 3VZD - UUL C15 H11 Cl N2 O S c1cc(ccc1c....
3 3VZB - SQS C18 H37 N O2 CCCCCCCCCC....
4 4V24 Ki = 4.3 nM GYR C27 H31 N O4 S Cc1cc(cc(c....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3VZC - UUL C15 H11 Cl N2 O S c1cc(ccc1c....
2 3VZD - UUL C15 H11 Cl N2 O S c1cc(ccc1c....
3 3VZB - SQS C18 H37 N O2 CCCCCCCCCC....
4 4V24 Ki = 4.3 nM GYR C27 H31 N O4 S Cc1cc(cc(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GYR; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 GYR 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4V24; Ligand: GYR; Similar sites found: 88
This union binding pocket(no: 1) in the query (biounit: 4v24.bio2) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO5 PIH 0.0008625 0.48172 None
2 4V2O CLQ 0.0186 0.41087 None
3 3B9Z CO2 0.004763 0.43942 1.07817
4 2OCI TYC 0.01024 0.43102 1.5748
5 4MZU TYD 0.02435 0.4107 1.60256
6 4RW3 PLM 0.04142 0.41 1.65563
7 4S00 AKR 0.03106 0.4026 1.88679
8 4F5Z BEZ 0.01543 0.41942 2.00669
9 3X27 TRP 0.03347 0.4027 2.08955
10 3HYW DCQ 0.01661 0.42125 2.15633
11 4CJN QNZ 0.02098 0.41263 2.15633
12 2Q8H TF4 0.02488 0.41179 2.15633
13 2Z9I GLY ALA THR VAL 0.03181 0.40667 2.16049
14 5ERM 210 0.03038 0.40331 2.20386
15 1RV1 IMZ 0.01217 0.41201 2.35294
16 4RQL SNE 0.02524 0.4087 2.42588
17 3KFF XBT 0.003246 0.45475 2.46914
18 3KFF ZBT 0.003246 0.45475 2.46914
19 2F2U M77 0.01673 0.40912 2.69542
20 1AUA BOG 0.03132 0.40325 2.7027
21 1A05 IPM 0.02917 0.40636 2.7933
22 2Y0I AKG 0.03654 0.40017 2.84091
23 2WA4 069 0.0198 0.40173 2.86533
24 5L6G XYP 0.01769 0.42056 2.96496
25 3GQT UFO 0.01037 0.41538 2.96496
26 1V9T SIN ALA PRO ALA NIT 0.02812 0.40572 3.01205
27 1Z6K OAA 0.02138 0.40766 3.07167
28 3AQT RCO 0.03644 0.40434 3.26531
29 3NV6 CAM 0.01961 0.40163 3.50404
30 3ZJQ NCA 0.01755 0.41126 3.58974
31 1JL0 PUT 0.0419 0.40036 3.59281
32 4Q0K GA3 0.01769 0.40052 3.7037
33 4EUO ABU 0.01704 0.40534 3.75
34 4R33 SAH 0.006436 0.40591 3.77358
35 4R33 TRP 0.006436 0.40591 3.77358
36 1XX4 BAM 0.02849 0.41365 3.83142
37 5LUN OGA 0.007607 0.43548 3.97727
38 5UGW GSH 0.01841 0.44029 4
39 2VFT SOR 0.005427 0.43341 4.31267
40 5E89 TD2 0.006825 0.4163 4.31655
41 4Y24 TD2 0.01696 0.40883 4.54545
42 4MRP GSH 0.02716 0.42749 4.58221
43 1DZT TPE 0.01869 0.41758 4.58221
44 1DZT ATY 0.03227 0.4054 4.58221
45 1XZ3 ICF 0.001669 0.49011 4.5977
46 2GKL PD2 0.01641 0.4057 4.84582
47 3ZGJ RMN 0.01688 0.41738 4.85175
48 4XMF HSM 0.01187 0.40781 4.8913
49 2VWA PTY 0.0142 0.42279 4.9505
50 3G08 FEE 0.01547 0.40618 5.05051
51 2BYC FMN 0.0007828 0.4696 5.10949
52 3TDC 0EU 0.00594 0.46279 5.12129
53 5A7V MAN 0.02626 0.40857 5.12129
54 2R5V HHH 0.021 0.40049 5.32213
55 2CHT TSA 0.02505 0.40837 5.51181
56 3BPX SAL 0.02992 0.40668 6.08108
57 1TV5 N8E 0.04707 0.40473 6.19946
58 5L8N 6RQ 0.0306 0.40403 6.25
59 1H8P PC 0.01436 0.4253 6.42202
60 1W31 SHO 0.03799 0.40043 6.43275
61 4J25 OGA 0.009412 0.43221 6.55022
62 1DQE BOM 0.007043 0.40531 6.56934
63 3KO0 TFP 0.04673 0.40639 6.93069
64 4X8D AVI 0.03807 0.40038 7.00809
65 5TVM PUT 0.02318 0.40557 7.05882
66 1Z03 OCH 0.004702 0.44637 7.27763
67 4JH6 FCN 0.01551 0.4149 7.97101
68 4WVW SLT 0.01583 0.42161 8.33333
69 1I06 TZL 0.01905 0.41462 8.33333
70 4J8T DOG 0.01471 0.40801 8.75912
71 1Y9Q MED 0.01386 0.42046 8.85417
72 5F6U 5VK 0.01862 0.41559 8.9172
73 5KEW 6SB 0.005526 0.44448 9.02778
74 5MPQ BLG 0.01689 0.40508 9.97305
75 3SHZ 5CO 0.02159 0.4036 9.97305
76 2Z77 NCA 0.01696 0.41727 10.0719
77 2IYG FMN 0.003163 0.44032 10.4839
78 4XCP PLM 0.01043 0.42528 10.5882
79 1YRX FMN 0.003027 0.4368 10.7438
80 4MGA 27L 0.0195 0.41518 10.9804
81 4TUZ 36J 0.0147 0.40803 10.9804
82 4MG8 27J 0.01297 0.40692 10.9804
83 4UBS DIF 0.01543 0.42642 11.5903
84 5VAD PRO 0.01765 0.40057 11.8598
85 1I7M PUT 0.03844 0.4036 13.4328
86 5N53 8NB 0.03655 0.40129 14.8718
87 4REI 3MV 0.0226 0.41254 16.5563
88 3KP6 SAL 0.006344 0.45162 19.8675
Pocket No.: 2; Query (leader) PDB : 4V24; Ligand: GYR; Similar sites found: 37
This union binding pocket(no: 2) in the query (biounit: 4v24.bio1) has 39 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5CHR 4NC 0.03029 0.41361 None
2 1J78 VDY 0.03405 0.40488 1.88679
3 3RGA LSB 0.01885 0.40366 2.12014
4 5T96 79J 0.04779 0.40104 2.63158
5 4DKX GDP 0.02037 0.41264 2.69542
6 5U9J GER 0.01984 0.42148 2.95858
7 3NJQ NJQ 0.007766 0.42197 3.62694
8 1JAY F42 0.03357 0.4015 3.77358
9 4QVX 3CQ 0.01372 0.40071 4.19162
10 3RLF MAL 0.03953 0.40146 4.31267
11 1POC GEL 0.006793 0.42109 4.47761
12 5T7I LAT NAG GAL 0.01225 0.43449 4.51613
13 2HFN FMN 0.008193 0.41731 4.57516
14 5HCN DAO 0.02422 0.41681 4.58221
15 4K7O EKZ 0.03116 0.41319 4.7619
16 4ZGM 32M 0.03316 0.41869 4.91803
17 2AGC DAO 0.01702 0.42069 5.55556
18 2QYK NPV 0.04893 0.40028 5.67164
19 2XN5 FUN 0.01528 0.41901 5.71429
20 5MOB A8S 0.01652 0.41728 6.19946
21 1L0I PSR 0.04749 0.40746 6.41026
22 1OFL NGK GCD 0.03434 0.40867 6.469
23 3ZPG 5GP 0.03615 0.40068 6.73854
24 5M8T 0TR 0.04866 0.40041 6.73854
25 1OW4 2AN 0.02529 0.40782 6.97674
26 2AXR ABL 0.01981 0.42205 7.15706
27 5N8V KZZ 0.02273 0.41411 7.24638
28 1SZO CAX 0.04368 0.40425 7.7821
29 1ZOY UQ1 0.04824 0.40249 8.73786
30 5H9Q TD2 0.009178 0.44582 9.03226
31 3OGN 3OG 0.01973 0.40271 10.4839
32 4BPZ GLC BGC BGC 0.037 0.40298 11.3281
33 1QKQ MAN 0.008214 0.43179 11.9718
34 4YSX EPH 0.01299 0.40177 12.8205
35 5OCA 9QZ 0.01279 0.45692 15.0794
36 4I67 G G G RPC 0.02798 0.40557 29.8851
37 5TPU TYD 0.03927 0.40855 31.6547
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