FAIRMol

NMT-TY0959

Pose ID 8432 Compound 527 Pose 302

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-TY0959
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
24.0 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.84, Jaccard 0.64, H-bond role recall 0.71
Burial
84%
Hydrophobic fit
71%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.126 kcal/mol/HA) ✓ Good fit quality (FQ -10.51) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ High strain energy (24.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-30.408
kcal/mol
LE
-1.126
kcal/mol/HA
Fit Quality
-10.51
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.27
cLogP
Strain ΔE
24.0 kcal/mol
SASA buried
84%
Lipo contact
71% BSA apolar/total
SASA unbound
647 Ų
Apolar buried
384 Ų

Interaction summary

HB 8 HY 8 PI 3 CLASH 3

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 rank3.873Score-30.408
Inter norm-1.141Intra norm0.015
Top1000noExcludedno
Contacts22H-bonds8
Artifact reasongeometry warning; 10 clashes; 2 protein clashes; moderate strain Δ 24.0
Residues
ALA111 ALA67 ARG154 ARG277 ASP233 ASP332 ASP88 GLU274 GLY199 GLY235 GLY236 GLY237 GLY276 HIS197 LYS69 PHE196 PRO275 SER195 SER200 THR132 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 overlap16Native recall0.84
Jaccard0.64RMSD-
HB strict5Strict recall0.56
HB same residue+role5HB role recall0.71
HB same residue6HB residue recall0.86

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
350 0.3629211958252925 -0.926251 -24.8853 2 13 0 0.00 0.00 - no Open
308 0.8712687604222177 -1.14475 -30.9484 7 15 0 0.00 0.00 - no Open
313 1.3142726160638258 -1.30957 -33.6603 12 15 0 0.00 0.00 - no Open
337 1.7652358533706136 -0.983958 -24.6706 6 21 0 0.00 0.00 - no Open
326 1.9773175739360493 -1.1336 -31.1195 10 21 0 0.00 0.00 - no Open
291 2.165473959343045 -1.26034 -34.3636 9 22 0 0.00 0.00 - no Open
301 2.480529293523874 -1.03512 -28.7525 9 12 0 0.00 0.00 - no Open
391 2.9008417563283935 -1.06217 -28.0759 7 15 0 0.00 0.00 - no Open
405 2.9806369013586718 -1.18262 -29.8648 6 15 0 0.00 0.00 - no Open
381 3.0321874169205607 -1.08611 -28.6887 6 16 0 0.00 0.00 - no Open
379 3.2808649478445537 -0.969429 -25.6956 10 17 0 0.00 0.00 - no Open
332 3.3588118370115048 -1.08116 -27.9486 7 17 0 0.00 0.00 - no Open
416 3.387046221950613 -0.924839 -25.7132 8 13 0 0.00 0.00 - no Open
334 3.429500560915679 -1.04914 -24.4852 8 15 0 0.00 0.00 - no Open
349 3.654496302035269 -0.850128 -21.98 8 14 0 0.00 0.00 - no Open
302 3.8731875216797746 -1.1408 -30.4082 8 22 16 0.84 0.71 - no Current
286 4.0813402406540185 -0.908062 -25.3939 13 15 0 0.00 0.00 - no Open
358 4.09740218547716 -0.710564 -18.8071 6 10 0 0.00 0.00 - no Open
336 4.132326379777683 -0.942975 -24.3804 7 17 0 0.00 0.00 - no Open
453 4.769829786717276 -1.02855 -27.026 8 17 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 -30.408kcal/mol
Ligand efficiency (LE) -1.1262kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.507
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 403.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.27
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 24.05kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -70.23kcal/mol
Minimised FF energy -94.28kcal/mol

SASA & burial

✓ computed
SASA (unbound) 647.1Ų
Total solvent-accessible surface area of free ligand
BSA total 540.7Ų
Buried surface area upon binding
BSA apolar 383.8Ų
Hydrophobic contacts buried
BSA polar 156.9Ų
Polar contacts buried
Fraction buried 83.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2551.0Ų
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 1389.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)