FAIRMol

NMT-TY0549

Pose ID 9132 Compound 411 Pose 324

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
T14
T. brucei ODC (G418 binding site) T. brucei G418 binding site
Ligand NMT-TY0549
PDB1NJJ↗

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
37.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.40, Jaccard 0.27, H-bond role recall 0.60
Burial
65%
Hydrophobic fit
68%
Reason: no major geometry red flags detected
2 protein-contact clashes 93% of hydrophobic surface is solvent-exposed (13/14 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 (-0.977 kcal/mol/HA) ✓ Good fit quality (FQ -9.12) ✓ Strong H-bond network (13 bonds) ✓ Good burial (65% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ Very high strain energy (37.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-26.388
kcal/mol
LE
-0.977
kcal/mol/HA
Fit Quality
-9.12
FQ (Leeson)
HAC
27
heavy atoms
MW
395
Da
LogP
-1.19
cLogP
Strain ΔE
37.4 kcal/mol
SASA buried
65%
Lipo contact
68% BSA apolar/total
SASA unbound
652 Ų
Apolar buried
289 Ų

Interaction summary

HB 13 HY 2 PI 0 CLASH 2 ⚠ Exposure 92%

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

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
93% of hydrophobic surface is solvent-exposed (13/14 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 14 Buried (contacted) 1 Exposed 13 LogP -1.19 H-bonds 13
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
Final rank3.302Score-26.388
Inter norm-0.916Intra norm-0.062
Top1000noExcludedno
Contacts13H-bonds13
Artifact reasongeometry warning; 7 clashes; 2 protein clashes; high strain Δ 37.4
Residues
ALA244 ARG242 ARG337 ASP243 ASP385 GLU384 LEU339 LYS247 MET386 PHE383 PRO245 PRO338 VAL336

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1NJJContacts15
PoseOpen native poseHB0
IFP residues
ARG22 ARG242 ARG337 ARG342 ASP243 ASP385 GLN341 GLU384 LEU25 LEU339 LEU382 PRO340 PRO344 SER282 THR241
Current overlap6Native recall0.40
Jaccard0.27RMSD-
HB strict2Strict recall0.33
HB same residue+role3HB role recall0.60
HB same residue3HB residue recall0.60

Protein summary

398 residues
Protein targetT14Atoms6140
Residues398Chains1
Residue summaryVAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:ORX602

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
263 1.9619591920682486 -1.07778 -26.3261 11 17 0 0.00 0.00 - no Open
307 1.973236208634677 -0.911074 -24.9818 7 15 0 0.00 0.00 - no Open
270 2.217204642698369 -1.21946 -32.7493 11 15 0 0.00 0.00 - no Open
352 2.4054056429997805 -0.963314 -22.8123 12 19 0 0.00 0.00 - no Open
276 2.4644015191207718 -1.23884 -34.4996 16 21 0 0.00 0.00 - no Open
287 2.4692123455684767 -0.887788 -22.8583 6 18 0 0.00 0.00 - no Open
293 2.5523531210354715 -1.25212 -32.8271 13 20 0 0.00 0.00 - no Open
264 3.2494165124044274 -1.31147 -36.2843 14 18 0 0.00 0.00 - no Open
377 3.300748553183803 -0.898096 -26.0956 7 13 0 0.00 0.00 - no Open
324 3.301523972802756 -0.915736 -26.3877 13 13 6 0.40 0.60 - no Current
239 4.313905727494139 -1.00534 -29.1414 16 16 0 0.00 0.00 - no Open
273 4.418567444093437 -1.2144 -31.3287 15 26 0 0.00 0.00 - no Open
284 4.844348523444292 -1.06372 -30.1625 10 15 0 0.00 0.00 - no Open
250 4.926468000366607 -1.2862 -36.0618 15 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 -26.388kcal/mol
Ligand efficiency (LE) -0.9773kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.118
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 395.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) -1.19
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 37.35kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -156.24kcal/mol
Minimised FF energy -193.59kcal/mol

SASA & burial

✓ computed
SASA (unbound) 652.1Ų
Total solvent-accessible surface area of free ligand
BSA total 423.3Ų
Buried surface area upon binding
BSA apolar 288.7Ų
Hydrophobic contacts buried
BSA polar 134.6Ų
Polar contacts buried
Fraction buried 64.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 68.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2381.5Ų
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 3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1391.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)