FAIRMol

Z49580011

Pose ID 9403 Compound 2579 Pose 595

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 Z49580011
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 high Native mixed SASA done
Strain ΔE
23.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.27, Jaccard 0.20, H-bond role recall 0.20
Burial
78%
Hydrophobic fit
91%
Reason: no major geometry red flags detected
1 protein-contact clashes 60% of hydrophobic surface is solvent-exposed (9/15 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 (-1.003 kcal/mol/HA) ✓ Good fit quality (FQ -8.86) ✓ Good H-bonds (5 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (91%) ✗ High strain energy (23.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-23.075
kcal/mol
LE
-1.003
kcal/mol/HA
Fit Quality
-8.86
FQ (Leeson)
HAC
23
heavy atoms
MW
418
Da
LogP
4.83
cLogP
Strain ΔE
23.9 kcal/mol
SASA buried
78%
Lipo contact
91% BSA apolar/total
SASA unbound
616 Ų
Apolar buried
440 Ų

Interaction summary

HB 5 HY 5 PI 0 CLASH 1 ⚠ Exposure 60%

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
60% of hydrophobic surface is solvent-exposed (9/15 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 15 Buried (contacted) 6 Exposed 9 LogP 4.83 H-bonds 5
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
Final rank2.932Score-23.075
Inter norm-1.003Intra norm0.000
Top1000noExcludedno
Contacts9H-bonds5
Artifact reasongeometry warning; 8 clashes; 2 protein clashes; moderate strain Δ 23.9
Residues
ARG22 ARG342 ASN20 CYS26 GLN341 GLU343 SER282 THR21 THR285

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 overlap4Native recall0.27
Jaccard0.20RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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
598 1.8249022103544557 -1.07708 -21.5511 2 17 0 0.00 0.00 - no Open
595 2.9316105529827015 -1.0033 -23.075 5 9 4 0.27 0.20 - no Current
592 3.1335927947605646 -1.18314 -26.8681 7 15 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 -23.075kcal/mol
Ligand efficiency (LE) -1.0033kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.855
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 418.1Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.83
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.86kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 113.14kcal/mol
Minimised FF energy 89.28kcal/mol

SASA & burial

✓ computed
SASA (unbound) 616.0Ų
Total solvent-accessible surface area of free ligand
BSA total 481.8Ų
Buried surface area upon binding
BSA apolar 440.1Ų
Hydrophobic contacts buried
BSA polar 41.6Ų
Polar contacts buried
Fraction buried 78.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 91.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2487.0Ų
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 3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1412.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)