FAIRMol

NMT-TY0920

Pose ID 8425 Compound 544 Pose 295

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-TY0920
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
37.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.74, Jaccard 0.64, H-bond role recall 0.57
Burial
77%
Hydrophobic fit
78%
Reason: no major geometry red flags detected
2 protein-contact clashes 78% of hydrophobic surface is solvent-exposed (14/18 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.143 kcal/mol/HA) ✓ Good fit quality (FQ -10.79) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Very high strain energy (37.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-32.010
kcal/mol
LE
-1.143
kcal/mol/HA
Fit Quality
-10.79
FQ (Leeson)
HAC
28
heavy atoms
MW
418
Da
LogP
2.31
cLogP
Strain ΔE
37.9 kcal/mol
SASA buried
77%
Lipo contact
78% BSA apolar/total
SASA unbound
646 Ų
Apolar buried
391 Ų

Interaction summary

HB 7 HY 2 PI 2 CLASH 2 ⚠ Exposure 77%

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
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
78% of hydrophobic surface is solvent-exposed (14/18 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 18 Buried (contacted) 4 Exposed 14 LogP 2.31 H-bonds 7
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
Final rank3.616Score-32.010
Inter norm-0.981Intra norm-0.162
Top1000noExcludedno
Contacts17H-bonds7
Artifact reasongeometry warning; 13 clashes; 2 protein clashes; high strain Δ 37.9
Residues
ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 GLU274 GLY199 GLY201 GLY236 GLY237 GLY276 HIS197 HIS333 LYS69 SER200 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 overlap14Native recall0.74
Jaccard0.64RMSD-
HB strict3Strict recall0.33
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
302 0.5239567590025211 -1.18433 -30.604 9 13 0 0.00 0.00 - no Open
319 0.9940520654587742 -0.944043 -25.3008 5 13 0 0.00 0.00 - no Open
320 1.0669444827431311 -0.878088 -31.4505 3 16 0 0.00 0.00 - no Open
345 1.1134646347622539 -0.877657 -23.1229 3 15 0 0.00 0.00 - no Open
369 1.570299553280359 -0.935163 -25.1037 6 14 0 0.00 0.00 - no Open
285 1.846962516011115 -1.10054 -35.0271 11 16 0 0.00 0.00 - no Open
333 2.430240854014312 -0.961348 -34.1213 11 17 0 0.00 0.00 - no Open
313 2.7355217655896267 -0.945999 -28.0195 7 18 0 0.00 0.00 - no Open
388 3.1357764599548372 -1.01979 -35.0482 6 16 0 0.00 0.00 - no Open
366 3.33349022232488 -1.04252 -32.8619 6 15 0 0.00 0.00 - no Open
313 3.427850034969361 -1.24397 -30.3675 11 26 0 0.00 0.00 - no Open
342 3.492057571577017 -0.785111 -22.7794 9 15 0 0.00 0.00 - no Open
295 3.616137840018539 -0.981468 -32.0097 7 17 14 0.74 0.57 - no Current
437 3.855523120955258 -0.937716 -27.4849 10 13 0 0.00 0.00 - no Open
349 4.8296015227220686 -0.681525 -25.7042 8 9 0 0.00 0.00 - no Open
361 5.231781681702861 -0.899682 -33.3801 11 16 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 -32.010kcal/mol
Ligand efficiency (LE) -1.1432kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.792
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 417.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.31
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 37.89kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -24.39kcal/mol
Minimised FF energy -62.28kcal/mol

SASA & burial

✓ computed
SASA (unbound) 646.2Ų
Total solvent-accessible surface area of free ligand
BSA total 500.1Ų
Buried surface area upon binding
BSA apolar 391.2Ų
Hydrophobic contacts buried
BSA polar 108.9Ų
Polar contacts buried
Fraction buried 77.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2585.6Ų
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 1374.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)