FAIRMol

TC483

Pose ID 5626 Compound 3161 Pose 208

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
T09
L. major DHFR-TS L. major
Ligand TC483

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
46.2 kcal/mol
Protein clashes
0
Internal clashes
17
Native overlap
contact recall 0.57, Jaccard 0.43, H-bond role recall 0.17
Burial
82%
Hydrophobic fit
86%
Reason: 17 internal clashes, strain 46.2 kcal/mol
strain ΔE 46.2 kcal/mol 17 intramolecular clashes 59% of hydrophobic surface appears solvent-exposed (19/32 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.436 kcal/mol/HA) ✓ Good fit quality (FQ -4.58) ✓ Good H-bonds (4 bonds) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (86%) ✗ Extreme strain energy (46.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (17)
Score
-17.878
kcal/mol
LE
-0.436
kcal/mol/HA
Fit Quality
-4.58
FQ (Leeson)
HAC
41
heavy atoms
MW
559
Da
LogP
5.24
cLogP
Final rank
4.5171
rank score
Inter norm
-0.648
normalised
Contacts
19
H-bonds 5
Strain ΔE
46.2 kcal/mol
SASA buried
82%
Lipo contact
86% BSA apolar/total
SASA unbound
925 Ų
Apolar buried
648 Ų

Interaction summary

HBA 4 HY 8 PI 1 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 2.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
Name3CL9Contacts21
PoseOpen native poseHB0
IFP residues
NDP301 ALA32 ARG97 ASP52 GLY157 ILE45 LEU94 LYS57 MET53 PHE55 PHE56 PHE91 PRO88 SER86 THR180 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap12Native recall0.57
Jaccard0.43RMSD-
HB strict2Strict recall0.29
HB same residue+role1HB role recall0.17
HB same residue1HB residue recall0.17

Protein summary

511 residues
Protein targetT09Atoms8170
Residues511Chains2
Residue summaryLEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224

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:NDP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
243 3.7127852995163635 -0.780171 -25.6506 6 16 0 0.00 0.00 - no Open
188 4.2676262282320385 -0.741775 -24.2765 10 17 0 0.00 0.00 - no Open
208 4.51709479773615 -0.64753 -17.8777 5 19 12 0.57 0.17 - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -17.878kcal/mol
Ligand efficiency (LE) -0.4360kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.582
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 41HA

Physicochemical properties
Molecular weight 558.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.24
Lipinski: ≤ 5
Rotatable bonds 12

Conformational strain (MMFF94s)
Strain energy (ΔE) 46.19kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 153.91kcal/mol
Minimised FF energy 107.72kcal/mol

SASA & burial

✓ computed
SASA (unbound) 925.2Ų
Total solvent-accessible surface area of free ligand
BSA total 755.1Ų
Buried surface area upon binding
BSA apolar 648.0Ų
Hydrophobic contacts buried
BSA polar 107.1Ų
Polar contacts buried
Fraction buried 81.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 85.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3538.2Ų
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 4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1681.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)