FAIRMol

NMT-TY0929

Pose ID 8426 Compound 484 Pose 296

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-TY0929
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
32.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.79, Jaccard 0.71, H-bond role recall 0.57
Burial
76%
Hydrophobic fit
69%
Reason: no major geometry red flags detected
1 protein-contact clashes 41% of hydrophobic surface appears solvent-exposed (7/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.131 kcal/mol/HA) ✓ Good fit quality (FQ -10.55) ✓ Strong H-bond network (13 bonds) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (69%) ✗ Very high strain energy (32.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-30.529
kcal/mol
LE
-1.131
kcal/mol/HA
Fit Quality
-10.55
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.27
cLogP
Strain ΔE
32.4 kcal/mol
SASA buried
76%
Lipo contact
69% BSA apolar/total
SASA unbound
615 Ų
Apolar buried
324 Ų

Interaction summary

HB 13 HY 2 PI 2 CLASH 1 ⚠ Exposure 41%

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
⚠️Partial hydrophobic solvent exposure
41% of hydrophobic surface appears solvent-exposed (7/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17 Buried (contacted) 10 Exposed 7 LogP 2.27 H-bonds 13
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank6.200Score-30.529
Inter norm-1.056Intra norm-0.074
Top1000noExcludedno
Contacts17H-bonds13
Artifact reasongeometry warning; 14 clashes; 5 protein clashes; high strain Δ 32.4
Residues
ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 GLU274 GLY199 GLY201 GLY236 GLY237 GLY276 HIS197 LYS69 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
Jaccard0.71RMSD-
HB strict5Strict recall0.56
HB same residue+role4HB role recall0.57
HB same residue4HB residue recall0.57

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
346 0.35538722495997677 -0.978913 -25.6036 2 13 0 0.00 0.00 - no Open
293 1.274900942951345 -1.03583 -28.5719 7 12 0 0.00 0.00 - no Open
323 1.3627403067812827 -0.906394 -18.7308 3 16 0 0.00 0.00 - no Open
375 2.0500114754417558 -1.04631 -29.6312 5 15 0 0.00 0.00 - no Open
318 2.0823117440239103 -1.13317 -28.9361 12 15 0 0.00 0.00 - no Open
322 2.294639162656896 -0.986167 -29.4161 5 20 0 0.00 0.00 - no Open
441 2.5220455662358785 -0.89302 -25.8372 8 15 0 0.00 0.00 - no Open
338 2.659289984590069 -0.997905 -24.9728 12 15 0 0.00 0.00 - no Open
392 2.7685730244744846 -1.12247 -31.1016 6 15 0 0.00 0.00 - no Open
333 3.6903577688505305 -0.859379 -21.1312 9 16 0 0.00 0.00 - no Open
343 3.8983164634663794 -0.849572 -21.6991 9 14 0 0.00 0.00 - no Open
372 3.9624227153920875 -1.10356 -28.0126 4 18 0 0.00 0.00 - no Open
282 4.021294943242523 -1.239 -35.8435 9 17 0 0.00 0.00 - no Open
316 4.705477255827921 -1.17836 -28.5533 9 21 0 0.00 0.00 - no Open
287 4.830955251729373 -1.16188 -25.6924 10 15 0 0.00 0.00 - no Open
353 5.092204702816937 -0.795238 -22.7627 7 12 0 0.00 0.00 - no Open
272 5.40909853377186 -0.937498 -19.6641 16 12 0 0.00 0.00 - no Open
409 5.703467463727863 -0.909529 -26.8524 10 16 1 0.05 0.00 - no Open
296 6.199766084150915 -1.0563 -30.5291 13 17 15 0.79 0.57 - no Current

Molecular metrics

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

Scoring & efficiency
Docking score -30.529kcal/mol
Ligand efficiency (LE) -1.1307kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.549
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) 32.35kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -36.02kcal/mol
Minimised FF energy -68.37kcal/mol

SASA & burial

✓ computed
SASA (unbound) 614.7Ų
Total solvent-accessible surface area of free ligand
BSA total 466.5Ų
Buried surface area upon binding
BSA apolar 323.7Ų
Hydrophobic contacts buried
BSA polar 142.8Ų
Polar contacts buried
Fraction buried 75.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 69.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2504.4Ų
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 1410.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)