Receptor
PDB id Resolution Class Description Source Keywords
5XCO 1.25 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF HUMAN K-RAS G12D MUTANT IN COMPLEX WITH CYCLIC INHIBITORY PEPTIDE HOMO SAPIENS HYDROLASE COMPLEX INHIBITOR SMALL GTPASE ONCOGENE SIGNAHYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: CRYSTAL STRUCTURE OF A HUMAN K-RAS G12D MUTANT IN C WITH GDP AND THE CYCLIC INHIBITORY PEPTIDE KRPEP-2D ACS MED CHEM LETT V. 8 732 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:201;
Valid;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
EDO A:202;
Invalid;
none;
submit data
62.068 C2 H6 O2 C(CO)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5O2T 2.19 Å EC: 7.-.-.- HUMAN KRAS IN COMPLEX WITH DARPIN K27 HOMO SAPIENS KRAS RAS SIGNALLING DARPIN NUCLEOTIDE EXCHANGE SIGNALING
Ref.: STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF A DAR INHIBITS RAS NUCLEOTIDE EXCHANGE. NAT COMMUN V. 8 16111 2017
Members (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 293 families.
1 5WFO - 5UU C19 H16 Cl F N2 c1cc(ccc1N....
2 6FA3 Kd = 0.038 uM D1Z C30 H36 N4 O5 CN(C)Cc1cc....
3 5WFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
4 5O2T Kd = 3.9 nM GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
5 5WPM - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
6 5WFR - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
7 5UFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
8 6AMB - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
9 6FA1 - D2Z C20 H25 N2 O4 C[NH+](C)C....
10 5UFE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
11 5WFP - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
12 5WHB - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
13 5WPL - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
14 5XCO - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
15 1NVU - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
16 5WHE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
70% Homology Family (34)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 250 families.
1 5WFO - 5UU C19 H16 Cl F N2 c1cc(ccc1N....
2 6FA3 Kd = 0.038 uM D1Z C30 H36 N4 O5 CN(C)Cc1cc....
3 5WFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
4 5O2T Kd = 3.9 nM GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
5 5WPM - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
6 5WFR - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
7 5UFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
8 6AMB - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
9 6FA1 - D2Z C20 H25 N2 O4 C[NH+](C)C....
10 5UFE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
11 5WFP - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
12 5WHB - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
13 5WPL - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
14 5XCO - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
15 1NVU - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
16 5WHE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
17 3KUC - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
18 1C1Y - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
19 5TAR - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
20 4DXA - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
21 4HDO - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
22 5E95 Kd = 15.7 nM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
23 3CF6 - SP1 C10 H12 N5 O5 P S c1nc(c2c(n....
24 6FA4 Kd = 0.051 uM D1W C23 H25 N3 O3 CN(C)Cc1cc....
25 2C5L - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
26 4K81 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
27 1LFD - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
28 4KVG - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
29 1WQ1 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
30 3DDC - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
31 3KUD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
32 4URZ Kd = 3 mM VJP C11 H14 N2 O3 S c1cc(ccc1N....
33 4URX Kd = 1.3 mM HXY C11 H14 Br N c1cc(ccc1C....
34 4URY Kd = 6 mM RV1 C10 H12 N2 O3 S c1cc(ccc1N....
50% Homology Family (47)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 204 families.
1 3QBT - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
2 5WFO - 5UU C19 H16 Cl F N2 c1cc(ccc1N....
3 6FA3 Kd = 0.038 uM D1Z C30 H36 N4 O5 CN(C)Cc1cc....
4 5WFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
5 5O2T Kd = 3.9 nM GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
6 5WPM - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
7 5WFR - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
8 5UFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
9 6AMB - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
10 6FA1 - D2Z C20 H25 N2 O4 C[NH+](C)C....
11 5UFE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
12 5WFP - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
13 5WHB - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
14 5WPL - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
15 5XCO - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
16 1NVU - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
17 5WHE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
18 3KUC - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
19 1C1Y - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
20 5TAR - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
21 4DXA - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
22 4HDO - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
23 3MJH - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
24 5E95 Kd = 15.7 nM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
25 3CF6 - SP1 C10 H12 N5 O5 P S c1nc(c2c(n....
26 2CJW Kd = 2.5 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
27 6FA4 Kd = 0.051 uM D1W C23 H25 N3 O3 CN(C)Cc1cc....
28 2C5L - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
29 4K81 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
30 1LFD - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
31 4KVG - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
32 3TNF - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
33 1ZC4 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
34 1ZC3 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
35 2A9K - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
36 2A78 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
37 1WQ1 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
38 3TKL - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
39 3DDC - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
40 3KUD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
41 1TU3 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
42 1UAD Ka = 7260000 M^-1 GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
43 5O74 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
44 3SFV - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
45 4URZ Kd = 3 mM VJP C11 H14 N2 O3 S c1cc(ccc1N....
46 4URX Kd = 1.3 mM HXY C11 H14 Br N c1cc(ccc1C....
47 4URY Kd = 6 mM RV1 C10 H12 N2 O3 S c1cc(ccc1N....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GDP; Similar ligands found: 161
No: Ligand ECFP6 Tc MDL keys Tc
1 GDP 1 1
2 GTP 0.909091 1
3 GP3 0.881579 0.973684
4 GNH 0.858974 0.986667
5 9GM 0.839506 0.973684
6 GNP 0.839506 0.973684
7 G 0.828947 0.986486
8 5GP 0.828947 0.986486
9 G1R 0.82716 0.986667
10 GCP 0.82716 0.973684
11 GSP 0.817073 0.948718
12 GAV 0.797619 0.961039
13 GMV 0.792683 0.973684
14 G2P 0.77381 0.961039
15 G2R 0.770115 0.961039
16 GP2 0.756098 0.961039
17 GDC 0.747253 0.961039
18 GKE 0.747253 0.961039
19 GDD 0.747253 0.961039
20 GPG 0.741573 0.961039
21 G3D 0.732558 0.986486
22 ALF 5GP 0.729412 0.888889
23 Y9Z 0.728261 0.902439
24 G5P 0.723404 0.973684
25 GFB 0.72043 0.961039
26 GTG 0.72043 0.936709
27 GDR 0.72043 0.961039
28 G4P 0.715909 0.986486
29 G3A 0.712766 0.973684
30 6CK 0.712766 0.936709
31 GDP AF3 0.7 0.888889
32 ALF GDP 0.7 0.888889
33 GDP ALF 0.7 0.888889
34 YGP 0.698925 0.901235
35 GKD 0.697917 0.961039
36 JB2 0.697917 0.961039
37 GDX 0.690722 0.973684
38 GPD 0.690722 0.925
39 GMP 0.684211 0.88
40 0O2 0.666667 0.986486
41 JB3 0.656863 0.948718
42 NGD 0.650485 0.961039
43 DGI 0.636364 0.923077
44 GDP 7MG 0.636364 0.911392
45 U2G 0.634615 0.936709
46 GPX 0.634409 0.946667
47 G G 0.632653 0.948052
48 IDP 0.632184 0.972973
49 2MD 0.632075 0.891566
50 CAG 0.62963 0.880952
51 CG2 0.622642 0.936709
52 FEG 0.619048 0.879518
53 MGD 0.614679 0.891566
54 ZGP 0.613208 0.869048
55 GH3 0.612903 0.973333
56 3GP 0.611765 0.946667
57 MD1 0.607143 0.891566
58 PGD 0.59292 0.925
59 DGT 0.591398 0.923077
60 BGO 0.588785 0.924051
61 TPG 0.582609 0.840909
62 DBG 0.582609 0.948718
63 2GP 0.574713 0.96
64 FE9 0.570175 0.776596
65 GCP G 0.56 0.921053
66 A G 0.553571 0.935065
67 G A A A 0.553571 0.923077
68 MGP 0.553191 0.961039
69 U A G G 0.548673 0.935065
70 G4M 0.548387 0.880952
71 6G0 0.547368 0.961039
72 G1R G1R 0.542373 0.924051
73 P2G 0.527473 0.883117
74 PGD O 0.525 0.850575
75 ADP 0.522222 0.92
76 R5I 0.520833 0.946667
77 R7I 0.520833 0.946667
78 GGM 0.517544 0.901235
79 DGP 0.516484 0.910256
80 DG 0.516484 0.910256
81 P1G 0.516129 0.871795
82 G U 0.513274 0.9
83 G1G 0.508475 0.925
84 IMP 0.505495 0.959459
85 AKW 0.504425 0.890244
86 G C 0.504348 0.9
87 GPC 0.491525 0.879518
88 G7M 0.483871 0.948052
89 6AD 0.479592 0.841463
90 ATP 0.473684 0.92
91 HEJ 0.473684 0.92
92 G2Q 0.471154 0.961039
93 5FA 0.46875 0.92
94 AQP 0.46875 0.92
95 GTA 0.468468 0.936709
96 7DD 0.468085 0.906667
97 G G G RPC 0.466102 0.875
98 SGP 0.463158 0.82716
99 01G 0.462963 0.902439
100 HFD 0.459184 0.873418
101 B4P 0.457447 0.894737
102 AP5 0.457447 0.894737
103 A2D 0.456522 0.894737
104 6YZ 0.455446 0.896104
105 G G G C 0.455285 0.9125
106 5GP 5GP 0.454545 0.883117
107 ANP 0.454545 0.896104
108 ACQ 0.454545 0.896104
109 AT4 0.452632 0.884615
110 A G C C 0.451613 0.911392
111 APC G U 0.45082 0.886076
112 PRT 0.449541 0.959459
113 G U34 0.449153 0.888889
114 DG DG 0.448598 0.865854
115 ITT 0.447917 0.868421
116 BA3 0.446809 0.894737
117 C2E 0.444444 0.921053
118 PCG 0.444444 0.933333
119 35G 0.444444 0.933333
120 MGO 0.441176 0.864198
121 AN2 0.4375 0.907895
122 G C C C 0.4375 0.924051
123 M33 0.43299 0.883117
124 UCG 0.429688 0.911392
125 A G U 0.42963 0.888889
126 ACP 0.428571 0.896104
127 MGQ 0.424528 0.935897
128 AR6 0.424242 0.894737
129 7DT 0.424242 0.906667
130 APR 0.424242 0.894737
131 93A 0.42268 0.833333
132 A4P 0.420168 0.869048
133 G8D 0.42 0.875
134 AD9 0.42 0.896104
135 SAP 0.42 0.873418
136 AGS 0.42 0.873418
137 CA0 0.418367 0.896104
138 ATF 0.417476 0.884615
139 AGO 0.414634 0.888889
140 A G U U 0.414286 0.888889
141 NIA 0.413043 0.82716
142 MGV 0.412844 0.890244
143 TAT 0.411765 0.884615
144 T99 0.411765 0.884615
145 ADQ 0.411215 0.871795
146 A1R 0.411215 0.839506
147 RGT 0.410714 0.909091
148 CGP 0.409836 0.86747
149 C1Z 0.409091 0.986486
150 A 0.408602 0.893333
151 AMP 0.408602 0.893333
152 UP5 0.40678 0.873418
153 AMZ 0.406593 0.918919
154 C2R 0.406593 0.906667
155 JBT 0.405882 0.778947
156 A22 0.40566 0.907895
157 25L 0.405405 0.907895
158 ADX 0.40404 0.809524
159 8OD 0.401961 0.946667
160 50T 0.4 0.883117
161 4TC 0.4 0.851852
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5O2T; Ligand: GSP; Similar sites found with APoc: 83
This union binding pocket(no: 1) in the query (biounit: 5o2t.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 3WY9 GDP 5.32544
2 3U6B GDP 6.95187
3 4P3Y GDP 6.95187
4 2BVN GNP 6.95187
5 3U6K GDP 6.95187
6 1KK1 GNP 7.69231
7 5W75 GDP 8.28402
8 2WJG GDP 8.87574
9 3EC1 GDP 8.87574
10 4RD0 GDP 9.46746
11 5W7Q GDP 10.0592
12 5W76 GDP 10.0592
13 2WIC GNP 10.6509
14 1SKQ GDP 11.2426
15 2C77 GNP 11.8343
16 4J0Q GDP 12.426
17 1FQK ALF 13.9037
18 4TMZ GSP 15.3846
19 4NCN GTP 15.3846
20 4KAX GTP 16.568
21 6G14 G4P 16.568
22 3N5C GDP 17.9012
23 3PCR GTP 17.9012
24 4LC1 GDP 18.9349
25 5CK5 GDP 20.7101
26 2FH5 GTP 24.8521
27 1NRJ GTP 24.8521
28 5FG3 GDP 25.4438
29 1YRB GDP 27.8107
30 5YT0 GDP 28.4024
31 4M9Q GNP 28.4024
32 2A5F GTP 28.9941
33 2J59 GTP 31.9527
34 1RE0 GDP 32.5444
35 5KUT GDP 33.1361
36 2QN6 GDP 33.3333
37 1R4A GNP 33.3333
38 4DCT GDP 33.7278
39 1ZJ6 G3D 33.7278
40 1FQJ ALF 38.0952
41 3A1S GDP 38.4615
42 1FZQ GDP 39.645
43 4ZI2 GNP 39.645
44 4GOJ GNP 39.645
45 5DI3 GNP 41.4201
46 1M7B GTP 44.9704
47 3M1I GTP 46.7456
48 3WYF GTP 46.7456
49 3WYG GTP 46.7456
50 3GJX GTP 47.3373
51 3GJ4 GDP 47.3373
52 3GJ7 GDP 47.3373
53 3GJ5 GDP 47.3373
54 3REF GDP 47.3373
55 1IBR GNP 47.929
56 1GWN GTP 47.929
57 4HAT GNP 47.929
58 1WA5 GTP 47.929
59 3GJ3 GDP 47.929
60 5BXQ GDP 47.929
61 3RAB GNP 47.929
62 3CH5 GDP 47.929
63 2EW1 GNP 48.5207
64 1NF3 GNP 49.1124
65 5XC5 GTP 49.1124
66 4DKX GDP 49.7041
67 5UWJ GNP 49.7041
68 5UWI GNP 49.7041
69 5UWR GNP 49.7041
70 5DI9 GNP 49.7041
71 5LEF GTP 49.7041
72 5UWP GNP 49.7041
73 5UWQ GNP 49.7041
74 5DHF GNP 49.7041
75 5UWS GNP 49.7041
76 6CIT GNP 49.7041
77 5UWO GNP 49.7041
78 5UWT GNP 49.7041
79 5UWW GNP 49.7041
80 5UWU GNP 49.7041
81 5UWH GNP 49.7041
82 5UPK GNP 49.7041
83 2WKQ GTP 49.7041
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