FAIRMol

Z275025498

Pose ID 9178 Compound 760 Pose 370

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 Z275025498
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 mixed SASA done
Strain ΔE
35.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.40, Jaccard 0.33, H-bond role recall 0.20
Burial
66%
Hydrophobic fit
59%
Reason: no major geometry red flags detected
2 protein-contact clashes 65% of hydrophobic surface is solvent-exposed (11/17 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 (-0.855 kcal/mol/HA) ✓ Good fit quality (FQ -8.07) ✓ Good H-bonds (5 bonds) ✓ Deep burial (66% SASA buried) ✗ Very high strain energy (35.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-23.933
kcal/mol
LE
-0.855
kcal/mol/HA
Fit Quality
-8.07
FQ (Leeson)
HAC
28
heavy atoms
MW
430
Da
LogP
4.21
cLogP
Strain ΔE
35.1 kcal/mol
SASA buried
66%
Lipo contact
59% BSA apolar/total
SASA unbound
646 Ų
Apolar buried
249 Ų

Interaction summary

HB 5 HY 3 PI 0 CLASH 2 ⚠ Exposure 64%

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
65% of hydrophobic surface is solvent-exposed (11/17 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 17 Buried (contacted) 6 Exposed 11 LogP 4.21 H-bonds 5
Exposed fragments: phenyl (1/5 atoms exposed)phenyl (2/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
Final rank2.658Score-23.933
Inter norm-0.783Intra norm-0.071
Top1000noExcludedno
Contacts9H-bonds5
Artifact reasongeometry warning; 11 clashes; 1 protein clash; high strain Δ 35.1
Residues
ARG242 ARG337 ASP243 ASP385 GLU384 PHE383 THR241 VAL335 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
Jaccard0.33RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
HB same residue2HB residue recall0.40

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
381 0.4678678754036258 -1.1526 -33.9568 4 15 0 0.00 0.00 - no Open
360 0.5197055751298865 -0.90829 -27.5829 3 17 0 0.00 0.00 - no Open
447 1.219696433124539 -0.981399 -29.5048 3 18 0 0.00 0.00 - no Open
355 1.3063524923317955 -1.04791 -30.2735 11 20 0 0.00 0.00 - no Open
408 1.743798155616244 -1.05333 -31.9361 3 16 0 0.00 0.00 - no Open
329 1.7650189558589326 -1.04283 -32.4787 6 12 0 0.00 0.00 - no Open
379 1.969342891855111 -0.889133 -24.5333 2 11 0 0.00 0.00 - no Open
325 2.125064930305446 -1.21138 -36.9499 9 20 0 0.00 0.00 - no Open
370 2.6577378078182576 -0.783465 -23.9328 5 9 6 0.40 0.20 - no Current
401 2.8276500106851037 -0.751507 -24.4635 10 12 0 0.00 0.00 - no Open
339 3.4270672992810502 -0.865213 -25.4592 9 17 0 0.00 0.00 - no Open
388 3.555555808287048 -0.931199 -26.8835 15 17 0 0.00 0.00 - no Open
360 3.9357191430534906 -1.02887 -25.0561 14 17 0 0.00 0.00 - no Open
385 4.556515282102343 -0.781229 -24.3789 8 11 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 -23.933kcal/mol
Ligand efficiency (LE) -0.8547kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.069
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 429.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.21
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 35.09kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 57.45kcal/mol
Minimised FF energy 22.35kcal/mol

SASA & burial

✓ computed
SASA (unbound) 646.3Ų
Total solvent-accessible surface area of free ligand
BSA total 424.4Ų
Buried surface area upon binding
BSA apolar 249.3Ų
Hydrophobic contacts buried
BSA polar 175.1Ų
Polar contacts buried
Fraction buried 65.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 58.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2312.6Ų
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 3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1464.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)