FAIRMol

Z2694498001

Pose ID 9269 Compound 3915 Pose 461

DB SELECTIONDocking 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 Z2694498001
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
24.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.40, Jaccard 0.32, H-bond role recall 0.20
Burial
77%
Hydrophobic fit
81%
Reason: no major geometry red flags detected
1 protein-contact clashes 35% of hydrophobic surface appears solvent-exposed (6/17 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 (-0.905 kcal/mol/HA) ✓ Good fit quality (FQ -8.12) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ High strain energy (24.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-21.732
kcal/mol
LE
-0.905
kcal/mol/HA
Fit Quality
-8.12
FQ (Leeson)
HAC
24
heavy atoms
MW
317
Da
LogP
3.05
cLogP
Strain ΔE
24.9 kcal/mol
SASA buried
77%
Lipo contact
81% BSA apolar/total
SASA unbound
541 Ų
Apolar buried
338 Ų

Interaction summary

HB 6 HY 8 PI 0 CLASH 1 ⚠ Exposure 35%

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
⚠️Partial hydrophobic solvent exposure
35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17 Buried (contacted) 11 Exposed 6 LogP 3.05 H-bonds 6
Exposed fragments: phenyl (5/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank2.522Score-21.732
Inter norm-0.977Intra norm0.071
Top1000noExcludedno
Contacts10H-bonds6
Artifact reasongeometry warning; 14 clashes; 1 protein clash; moderate strain Δ 24.9
Residues
ALA334 ARG337 ASP243 ASP385 GLU384 LEU339 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
Jaccard0.32RMSD-
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
461 2.522456269801754 -0.976798 -21.7315 6 10 6 0.40 0.20 - no Current
441 3.775283001738127 -1.15981 -27.0515 12 9 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 -21.732kcal/mol
Ligand efficiency (LE) -0.9055kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.115
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 317.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.05
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 24.86kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 157.53kcal/mol
Minimised FF energy 132.67kcal/mol

SASA & burial

✓ computed
SASA (unbound) 541.3Ų
Total solvent-accessible surface area of free ligand
BSA total 418.3Ų
Buried surface area upon binding
BSA apolar 337.9Ų
Hydrophobic contacts buried
BSA polar 80.4Ų
Polar contacts buried
Fraction buried 77.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2416.4Ų
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 3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1393.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)