FAIRMol

Z49894143

Pose ID 6057 Compound 3225 Pose 639

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
T09
L. major DHFR-TS L. major
Ligand Z49894143

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
19.2 kcal/mol
Protein clashes
7
Internal clashes
7
Native overlap
contact recall 0.57, Jaccard 0.48, H-bond role recall 0.17
Burial
93%
Hydrophobic fit
82%
Reason: 7 internal clashes
7 protein-contact clashes 7 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.184 kcal/mol/HA) ✓ Good fit quality (FQ -10.45) ✓ Good H-bonds (4 bonds) ✓ Deep burial (93% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Moderate strain (19.2 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (11) ✗ Internal clashes (9)
Score
-27.223
kcal/mol
LE
-1.184
kcal/mol/HA
Fit Quality
-10.45
FQ (Leeson)
HAC
23
heavy atoms
MW
343
Da
LogP
4.67
cLogP
Strain ΔE
19.2 kcal/mol
SASA buried
93%
Lipo contact
82% BSA apolar/total
SASA unbound
549 Ų
Apolar buried
418 Ų

Interaction summary

HB 4 HY 24 PI 2 CLASH 7

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

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

HY · Hydrophobic contacts

CLASH · Clashes
Final rank1.657Score-27.223
Inter norm-1.096Intra norm-0.087
Top1000noExcludedno
Contacts16H-bonds4
Artifact reasongeometry warning; 9 clashes; 11 protein contact clashes
Residues
NDP301 ALA32 ARG48 ASP52 ILE182 ILE45 MET53 PHE55 PHE56 THR180 TRP47 TYR162 VAL156 VAL30 VAL31 VAL49

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
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
Jaccard0.48RMSD-
HB strict0Strict recall0.00
HB same residue+role1HB role recall0.17
HB same residue2HB residue recall0.33

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
657 0.8287109049828084 -1.36544 -32.0998 5 17 0 0.00 0.00 - no Open
639 1.657349021360132 -1.09624 -27.2228 4 16 12 0.57 0.17 - no Current
661 3.2786100253624912 -1.19441 -31.4459 10 13 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 -27.223kcal/mol
Ligand efficiency (LE) -1.1836kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.446
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 342.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.67
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 19.22kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 43.87kcal/mol
Minimised FF energy 24.64kcal/mol

SASA & burial

✓ computed
SASA (unbound) 548.8Ų
Total solvent-accessible surface area of free ligand
BSA total 512.1Ų
Buried surface area upon binding
BSA apolar 418.1Ų
Hydrophobic contacts buried
BSA polar 94.1Ų
Polar contacts buried
Fraction buried 93.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3213.1Ų
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 1670.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)