FAIRMol

NMT-TY0555

Pose ID 8378 Compound 515 Pose 248

DB fairmolDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T13
T. brucei ODC (Active site) T. brucei Active site
Ligand NMT-TY0555
PDB1F3T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
36.4 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.79, Jaccard 0.68, H-bond role recall 0.43
Burial
78%
Hydrophobic fit
68%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.391 kcal/mol/HA) ✓ Good fit quality (FQ -11.64) ✓ Strong H-bond network (14 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ Very high strain energy (36.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-27.814
kcal/mol
LE
-1.391
kcal/mol/HA
Fit Quality
-11.64
FQ (Leeson)
HAC
20
heavy atoms
MW
296
Da
LogP
-0.68
cLogP
Strain ΔE
36.4 kcal/mol
SASA buried
78%
Lipo contact
68% BSA apolar/total
SASA unbound
490 Ų
Apolar buried
260 Ų

Interaction summary

HB 14 HY 8 PI 2 CLASH 4

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank2.996Score-27.814
Inter norm-1.444Intra norm0.053
Top1000noExcludedno
Contacts18H-bonds14
Artifact reasongeometry warning; 7 clashes; 2 protein clashes; high strain Δ 36.4
Residues
ALA67 ARG277 ASP332 ASP88 CYS70 GLU274 GLY199 GLY235 GLY236 GLY237 GLY276 HIS197 LYS69 PHE196 PRO275 SER200 TYR331 TYR389

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1F3TContacts19
PoseOpen native poseHB0
IFP residues
ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 CYS70 GLU274 GLY236 GLY237 GLY276 HIS197 LYS69 PHE238 PRO275 SER200 TYR278 TYR331 TYR389
Current overlap15Native recall0.79
Jaccard0.68RMSD-
HB strict3Strict recall0.33
HB same residue+role3HB role recall0.43
HB same residue3HB residue recall0.43

Protein summary

411 residues
Protein targetT13Atoms6340
Residues411Chains1
Residue summaryVAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
291 1.1342832901296953 -1.47243 -28.1213 7 13 0 0.00 0.00 - no Open
308 1.1407956598243199 -1.47271 -28.0966 7 13 0 0.00 0.00 - no Open
287 1.425854450107728 -1.57638 -29.017 10 15 0 0.00 0.00 - no Open
294 1.4368563653499584 -1.58614 -29.0417 10 15 0 0.00 0.00 - no Open
340 1.5199875327590986 -1.30421 -24.1616 12 16 0 0.00 0.00 - no Open
325 1.8929444358902847 -1.09972 -20.59 10 11 0 0.00 0.00 - no Open
264 2.0213778030470935 -1.28263 -24.1424 8 15 0 0.00 0.00 - no Open
272 2.07930378903586 -1.19931 -21.6886 10 17 0 0.00 0.00 - no Open
288 2.272686469792997 -1.20072 -21.8379 10 17 0 0.00 0.00 - no Open
255 2.604134178216891 -1.55444 -29.5672 11 18 0 0.00 0.00 - no Open
395 2.618228131873109 -1.34198 -25.4179 10 16 0 0.00 0.00 - no Open
307 2.6395815071657873 -1.216 -22.6881 12 17 0 0.00 0.00 - no Open
324 2.719858307570968 -0.962258 -19.339 7 11 0 0.00 0.00 - no Open
272 2.890185804928903 -1.24872 -23.3539 7 15 0 0.00 0.00 - no Open
354 2.894301988851109 -1.46517 -27.278 13 19 0 0.00 0.00 - no Open
248 2.9955573621189955 -1.44392 -27.8137 14 18 15 0.79 0.43 - no Current
346 3.086475756889026 -1.42333 -26.6003 13 19 0 0.00 0.00 - no Open
299 3.1992481359795537 -1.24642 -23.7166 13 17 0 0.00 0.00 - no Open
285 3.2187089349618714 -1.29682 -23.427 10 17 0 0.00 0.00 - no Open
379 3.2560466957189305 -1.35838 -25.6607 9 16 1 0.05 0.00 - no Open
369 3.4560880962334983 -1.32647 -25.5936 9 16 1 0.05 0.00 - no Open
254 3.4642926757389616 -1.30203 -24.5606 9 15 0 0.00 0.00 - no Open
406 3.67636034041161 -1.29246 -24.4616 10 16 0 0.00 0.00 - no Open
333 3.717795610400825 -1.4146 -26.5109 10 14 0 0.00 0.00 - no Open
241 3.724783035797209 -1.26416 -21.7498 15 13 0 0.00 0.00 - no Open
251 3.7829044977730146 -1.35705 -25.1409 11 19 0 0.00 0.00 - no Open
330 3.7929991462566486 -0.942708 -18.8834 6 11 0 0.00 0.00 - no Open
241 4.010694369049239 -1.38136 -25.2742 11 19 0 0.00 0.00 - no Open
226 4.299065349056032 -1.39557 -26.9943 14 15 13 0.68 0.43 - no Open
257 4.359761779337785 -1.65662 -30.294 16 22 0 0.00 0.00 - no Open
274 4.532558280468934 -1.63443 -31.073 16 21 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -27.814kcal/mol
Ligand efficiency (LE) -1.3907kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.638
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 20HA

Physicochemical properties
Molecular weight 296.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.68
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 36.35kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -86.35kcal/mol
Minimised FF energy -122.70kcal/mol

SASA & burial

✓ computed
SASA (unbound) 490.1Ų
Total solvent-accessible surface area of free ligand
BSA total 382.6Ų
Buried surface area upon binding
BSA apolar 260.2Ų
Hydrophobic contacts buried
BSA polar 122.4Ų
Polar contacts buried
Fraction buried 78.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 68.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2410.2Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1385.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)