Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
17.3 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.79, Jaccard 0.60, H-bond role recall 0.29
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.023 kcal/mol/HA)
✓ Good fit quality (FQ -9.55)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (86% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ Moderate strain (17.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-27.629
kcal/mol
LE
-1.023
kcal/mol/HA
Fit Quality
-9.55
FQ (Leeson)
HAC
27
heavy atoms
MW
405
Da
LogP
3.97
cLogP
Interaction summary
HB 8
HY 12
PI 3
CLASH 2
Interaction summary
HB 8
HY 12
PI 3
CLASH 2
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 rank | 2.689 | Score | -27.629 |
|---|---|---|---|
| Inter norm | -1.115 | Intra norm | 0.091 |
| Top1000 | no | Excluded | no |
| Contacts | 21 | H-bonds | 8 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes | ||
| Residues |
ALA111
ALA67
ARG154
ARG277
ASP233
ASP332
ASP88
GLU274
GLY199
GLY235
GLY236
GLY237
GLY276
HIS197
LYS69
PHE196
SER195
SER200
THR132
TYR331
TYR389
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 1F3T | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA111
ALA67
ARG154
ARG277
ASP332
ASP88
CYS70
GLU274
GLY236
GLY237
GLY276
HIS197
LYS69
PHE238
PRO275
SER200
TYR278
TYR331
TYR389
| ||
| Current overlap | 15 | Native recall | 0.79 |
| Jaccard | 0.60 | RMSD | - |
| HB strict | 3 | Strict recall | 0.33 |
| HB same residue+role | 2 | HB role recall | 0.29 |
| HB same residue | 3 | HB residue recall | 0.43 |
Protein summary
411 residues
| Protein target | T13 | Atoms | 6340 |
|---|---|---|---|
| Residues | 411 | Chains | 1 |
| Residue summary | VAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 589 | 0.6327951476812925 | -0.835771 | -19.1893 | 0 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 589 | 1.4603448407455772 | -1.28409 | -32.1541 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 603 | 1.6561189607458788 | -0.91201 | -22.1367 | 2 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 604 | 2.688572672295505 | -1.11458 | -27.6292 | 8 | 21 | 15 | 0.79 | 0.29 | - | no | Current |
| 620 | 3.9769264438256893 | -1.13771 | -28.8668 | 12 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 602 | 4.470322151092261 | -0.896016 | -20.3387 | 7 | 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.
Scoring & efficiency
Docking score
-27.629kcal/mol
Ligand efficiency (LE)
-1.0233kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.547
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
404.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.97
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.25kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-25.38kcal/mol
Minimised FF energy
-42.63kcal/mol
SASA & burial
✓ computed
SASA (unbound)
660.9Ų
Total solvent-accessible surface area of free ligand
BSA total
565.8Ų
Buried surface area upon binding
BSA apolar
485.5Ų
Hydrophobic contacts buried
BSA polar
80.3Ų
Polar contacts buried
Fraction buried
85.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
85.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2615.2Ų
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
3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1408.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)